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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g58110.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
ttcgtg----atgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgtttt-tagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
||| |     || ||||||||  | ||   |  | |      | | | || |||||||| ||   ||  ||| ||| ||||| | |  |  |    | | |  ||||||||||||||||||||||||||||||| ||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| ||||
ttcatattacatcatgataatgtacatatagaactta-----tgatcgtgttggttatgctgtcatggatctgattcctttcatgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
ttcgtgatgatgataatacatatgagg-tgcctggtaatttaccatgctg-gttatgttgctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
   |     |   |   || |   ||| ||  |      | |||    |  ||||  ||    ||  ||| ||||| ||  | |  |  | ||  | |  ||||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||||||||| |
--tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcg-tctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
|    ||  |   | ||   | | |     |   |   ||  | | || ||  |     |  |   ||    ||  |  || | |  ||   || |   ||||||| || || || || ||  | || || || || ||| || | || || |||||||| ||||| ||  |||||||||||||||||||||| |||||||
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctga-agGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgttttt--agGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
   ||  |    |   | ||  |  || |  ||  | ||||      ||  |||   | | |   ||| | |  |||||   ||||    ||| ||||  ||||||| ||||| || |||||  | ||||| |||||||||||| | ||||| ||||| || ||||||||  | |||||||| || |||||||||||  | |
---gtacttcaaaattttcacgtatggcgattg-catttta------tgtatattgaggtataaatctgactcttttct---ctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttg-ctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
                    ||  | ||  |   | ||||  | ||  | | | ||||  | |     ||   |  |  |||   ||||  |  | || ||||||| |||||||| || ||  | || ||||||||||| ||| | ||||| |||||||| ||||||||| | ||||||||||| |||||||||||  | |
-------------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
ttcgtgatga-tgataatacatatgaggtgcctggtaatttaccatgctggttatg-ttgctgtgcgtctaatttctttcttaacttt-ttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
    |||  | | |       | || ||| | |       |    |||   |  || |  |||   |     ||| ||||||   |    |     |||| ||||||| ||||||||||||||| | ||||||||||| || ||  | || || ||  | || ||||||||  |||||||||| ||||||||||| ||||| |
---atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

upper sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
-ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgttttt--agGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
  |  |  | ||| |      |   |  ||| |   |  || |  || |   |||||    |  |   |    |||| |||    |     |  ||  |  |||| || ||||| ||||||||| | ||||| ||||| ||  || | || || ||| |||||||||||||  | |||||||||||||||||||| ||||| |
gcttatt-tcatggttggttgtgcaatttgctta-catgtttctttgataaatatgtcatagc-ctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

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|218488563|gb|FG963887.1|FG963887
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|58601852|gb|CK012380.1|CK012380
EST:     CAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAAGCAAGAGGGTG-TGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: CAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|6431609|gb|AU081261.1|AU081261
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAA-CTTCGATGAGATCTTGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|58690506|gb|CK079193.1|CK079193
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCA
EST: gi|58606356|gb|CK034389.1|CK034389
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTT
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTT
EST: gi|58659427|gb|CK048107.1|CK048107
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|24468795|gb|CA305744.1|CA305744
EST:     TTAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|163926984|gb|EG715158.1|EG715158
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGA
EST: gi|88388344|gb|CI627883.1|CI627883
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|33794240|gb|CF323010.1|CF323010
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|58689902|gb|CK078589.1|CK078589
EST:     GCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: GCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|44670933|gb|CR284367.1|CR284367
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|33693579|gb|CF321818.1|CF321818
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|6431644|gb|AU081296.1|AU081296
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|426067|gb|D21925.1|D21925
EST:     TCAGACAACATCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTAGAGGGAAACG
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|58590100|gb|CF988408.1|CF988408
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG
EST: gi|58669900|gb|CK058586.1|CK058586
EST:     TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACA
genomic: TCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACG

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: 73 (upstream exon), 75 (downstream exon)
Score: 118

AGACATGATTGCTCTGTCGTTTGTCCGTAAAGGATCAGATTTGGTTACCGTCAGACAACTTCTTGGACAGCATGCAAAGCGCATCAAGCTGATGTCAAAGgtttgtaatc ... ttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctggttatgttgctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
                               tcttaac  putative branch site (score: 118)
                         tttctttcttaacttt  CT-rich tract
                      taatttctttcttaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - atgatga
- - - - - - - - - - - - - gtgcctg
- - - - - - - - - - - - - - - - - - - - - catgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcgtc