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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG

Basic information

species Oryza sativa
transcript LOC_Os01g49690.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattga--tgctcacataccctgcaataccttt--------tttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG----------------------------
                      | | | |  |   |    ||||  |    ||| |||| || ||| | |    | ||||||   || |   || |||   | || |||         ||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||  ||||||||  |||||  |||                            
----------------------gactaaaagacattgttgttgt--tgttgttgcattt-ttatttgagtgtgatcatattggattgttatgatgccccatagtaacttcctttttcctttccagGTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGGTATGTCAGTTCTTTTGTCTTCAAGGAT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G055905_T08 (Zea mays), 3'ss of exon 1
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattga--tgctcacataccctgcaataccttt--------tttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
                      | | | |  |   |    ||||  |    ||| |||| || ||| | |    | ||||||   || |   || |||   | || |||         ||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||  ||||||||  |||||  |||
----------------------gactaaaagacattgttgttgt--tgttgttgcattt-ttatttgagtgtgatcatattggattgttatgatgccccatagtaacttcctttttcctttccagGTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G518717_T03 (Zea mays), 3'ss of exon 4
gtaagtttctgttcacatgtcagt------ccagataat-catagcattgtactaagcttgtatttcttt---tttcaatactgttatattga--tgctcacataccc----tgcaatacctttt---ttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
|| ||||   |||||||| |   |      ||||||| |   ||| ||| |||||   | ||||   |||   ||||| |      |||||||  || |   || |||    |    || |||||    ||||||||||||| || || |||||||||||||||||||| ||||| ||||||||| ||||||||  |||||  |||
gtgagttctcgttcacatatagattgacacccagatattgtgtagtattctactatagtagtatacatttgtatttcagtgtgaccatattgaattgttatgatgcccatattaacgtatcttttgttctccagGTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
      |   ||| |  ||    |  |  ||    | | |    | ||| ||||| |  |||      | | | | |  |  ||      || |  |   |      |||| ||||| |||||||| |||||||| || ||| | ||||||||||| |||||||| || || |||| ||| |  |||
-----ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgactt-----gagattatgaggtcaatagagtaattctttttgaa-----ttttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgt-tatat-tgatgctcaca--taccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
||| |||| |      || | | |    ||||||||    |      ||| ||  |  | |  |||      ||| || || ||| | |  ||  | ||||   | |     ||| ||||| ||||| || |||||||| || ||| ||||||||||||| |||||||| || || |||| ||| |  |||
gtatgttttt-----tatatgaattacaataatcattttgtaccctaaagttttaaaatataattttgggcttgtatagatatgaagttgtcaattcccctttgaaaa----tttgcagGTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G23310.1 (Glycine max), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgc--tcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
||| ||||||      |  | | |    |||||  |    ||   ||||  || ||     |  ||    |||  ||||   |||   |||  | ||||     |     ||| ||||| ||||| || |||||||| || ||| ||||||||||||| |||||||| || || |||| ||| |  |||
gtatgtttct-----taaatgaattacaataattcttttgtt-ccctaaatttttaaaatataattttggactcgtatagatatgaagtcaattcccctttggaaa----tttgcagGTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
||| ||||||      || | | |  | |||||  |    ||   ||||  || ||     |  ||     || ||  ||      | |    |  || ||       ||| ||||| ||||| || |||||||| || ||| ||||||||||||| |||||||| || || |||| ||| |  |||
gtatgtttct-----tatatgaatt-acataatttttctgtt-ccctaaatttttaaaatataattttgggctcttggatattaagtgatcgcctttggaaa------tttgcagGTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttt-----tcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
                 |||||     || ||    | | ||||   ||  || | ||| || ||     | || ||  |   | |||  | | | |  | ||   | | | | || ||||||||||||||||| || ||||||||||||||||||||||||||||| ||  |||||||||  || |  |||
----------------gtgtcacattgga-aacagcaacgttgtttcaacattatttttattattctgctttaaaacaatctgactgaaac-ctcgtgacttgt--ttcatctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATCTTAAGCTTCAACGAAAATATG

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------------gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagc-ttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttt-------tccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
                                                                               |  | |   ||   |    | || |  ||  |        | ||  |||| |   |||| | |  || || || |  |  ||||       ||   ||  || | || ||       | ||||||||||| ||||||||||||||||| |||||||||||||||||||| ||| ||||||||| ||| |  |||
gtatgcaccgtgtttttgtatgttcatgatagcttcttgatatcagtttgaattgttgggcccaagtgttttcttggattgggatctagtcgtccaagctgtgcccatgttggggtttctttaaaaagcatcagatttgtatggtctat-ctctgtttgtgatttctgagtatattgtgatgctttattgatctgtttcagGTGTGGTCTGCTCCTAATTATTGCTATAGATGTGGAAATGTTGCTTCGATATTAAGCTTCAATGAAAATATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88486727|gb|CI423998.1|CI423998
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88508989|gb|CI436495.1|CI436495
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88989163|gb|CI042276.1|CI042276
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86253096|gb|CI058021.1|CI058021
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|163921174|gb|EG710163.1|EG710163
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|218484413|gb|FG953190.1|FG953190
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86832994|gb|CI333593.1|CI333593
EST:     AAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: AAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88560342|gb|CI490996.1|CI490996
EST:     CAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: CAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88969389|gb|CI382928.1|CI382928
EST:     AGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: AGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88534514|gb|CI463241.1|CI463241
EST:     TTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|27577318|gb|CB000013.1|CB000013
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86870962|gb|CI326781.1|CI326781
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|431829|gb|D23910.1|D23910
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGGTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88486874|gb|CI424145.1|CI424145
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|325493557|gb|JG458081.1|JG458081
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|218492898|gb|FG955355.1|FG955355
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|27577630|gb|CB000325.1|CB000325
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86422413|gb|CI059986.1|CI059986
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|88472189|gb|CI409460.1|CI409460
EST:     AAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: AAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86419470|gb|CI054271.1|CI054271
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|3767660|gb|AU031687.1|AU031687
EST:     TGGTTCAGGAAGGCTTAAAGTNCATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACNGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|51946060|gb|CV152401.1|CV152401
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|86429383|gb|CI076064.1|CI076064
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|89180552|gb|CI044831.1|CI044831
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
EST: gi|29686455|gb|CB682730.1|CB682730
EST:     TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT                         GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA
genomic: TGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 72 (downstream exon)
Score: 41

TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACTgtaagtttct ... ttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG
                       tgctcac  putative branch site (score: 41)
                                         taccttttttcc  putative PPT
       aatactgttatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG