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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT

Basic information

species Physcomitrella patens
transcript PP1S17_306V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g10340.1 (Oryza sativa), 3'ss of exon 1
----gtaacgtcc-gctggctgt-ctgagctctttacgacagtcgaatgtgtaa----tttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT
    ||  | ||| ||   | || ||   ||| |        |   |  |  ||     |||||||||    | || |       |  | |       |  | | | | |  | ||||| ||||| |||||  | |||||||||||||||||||||||||| ||       ||||    |  |    | || |||||||| ||  |||| ||   ||||
gtgagtgccctcctgcccaccgttctctcctcctcctcctgcttagagatccaaaccccttcatttttactcgctagtcgctacatgggttgttgatgcagctttgcatttct-tgcagCGTCGATCCCTTTGCTAAGAAGGACTGGTATGATATCAAGGCCCCGTCGGTGTTCAATGTGCGGAACATCGGCAAGACCCTCGTGTCCAGGACACAGGGT

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G013457_T01 (Zea mays), 3'ss of exon 1
gtaa---cgtccgctggctgtctgagctctttacgacagtcg-aatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgt-gcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGC-TTGGGAAGACCCTTGTCACCAGAACCGCGGGT
||||    |   ||  | | |    | |||| ||  |  ||    |   |   ||| ||| || ||| |  ||  | |    | |    || |   ||     | || |  ||| ||||| |||||||| ||||||||||||||||| |||||||| ||      ||||| |     |   | |||||||||| || ||  |||| ||   ||||
gtaagtttgcttgcatgttcttcccgttcttcacatctatctcggtcaattgcttcgtttctg-gagcttctgctgatgc--ggttgtgtgtctgtgttccttttgtcttacagCGTCGATCCCTTCTCTAAGAAGGACTGGTATGACATCAAGGCCCCATCGGTCTTCA-GTGTGCGCAACATTGGGAAGACTCTCGTGTCCAGGACACAGGGT

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G703354_T01 (Zea mays), 3'ss of exon 1
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGC-TTGGGAAGACCCTTGTCACCAGAACCGCGGGT
         |   ||| |||    || |    |   |    | ||    |        ||  ||| |     ||  ||  |    || | || |     |  |||||||||| || || |||  |||||||||| |||||||||||||||||||      ||||| ||    |   | | || |||||||| ||  |||| ||   ||| 
---------gtgagctatctcccttcctcgtcatctttcgttctgcggatatgaaaccgttggttctgacccgtccct--tggtgtggccacatctcttt--tgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCA-GCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G34670.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT
               |   | | || | | |   | |  |||    |  ||  |  |||| |  | |  |  || |  |  |       |   |||  |    ||||||||| || ||||||||||||||||| ||||||||  | |||||||||    | |||||| | | |    |||||||||| |||||  |||| ||   ||||
--------------gtaagtaacctatgtcctg-aataaaattctcagatttctaattgtaatctgtatatagtgttcgtgattgaattgttatggatg----gtgcagTGTTGATCCCTTCTCCAAGAAGGATTGGTATGACGTGAAGGCTCCTGGTTCTTTCACGAACAGGAATGTTGGGAAGACTCTTGTTTCCAGGACTCAGGGT

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP08964 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgac-gacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGG-AAGACCCTTGTCACCAGAACCGCGGGT
                                            |||| |      |  |  |     | |     |  ||  ||   | | |  |      | | ||||    ||||||||| ||||||||||||||||||| |||||||| || | ||  |||||      |   | |||| |||||||| || ||||| ||   ||||
--------------------------------------------gtaagtcggccatc-tctgcgcccgcgacccccacctcgctcacctggctcgttttctgcgcgcagCTCGGACCCCTTCGCCAAGAAGGACTGGTATGACATCAAGGCGCCCACCATGTTCAC-TGTCCGCAACGTGGGCAAGACCCTGGTGACCAGGACGCAGGGT

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11589 (Selaginella moellendorffii), 3'ss of exon 2
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattga---gggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT
                                                          || |||  |||     |  || |||   |||||   | |        |   |||||||||||| |||||||||||||| ||||| ||| |||||||      ||| ||||          | | |||||||| ||||| || |||||   ||| 
----------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttctt-----ctttcctcagTGTCGACCCTTTCTCCAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

upper sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattga---gggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT
                                                          || |||  |||     |  || |||   |||||   | |        |   |||||||||||| ||||| |||||||| ||||| ||| |||||||      ||| ||||          | | |||||||| ||||| || |||||   ||| 
----------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttctt-----ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

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|208399084|gb|DC904493.1|DC904493
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTTCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208344601|gb|DC909160.1|DC909160
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162268511|gb|FC444384.1|FC444384
EST:     GGAAGAACAAGCGCGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGAAGAACAAGCG-GATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208389506|gb|DC929431.1|DC929431
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18332464|gb|BJ164477.1|BJ164477
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18358607|gb|BJ190666.1|BJ190666
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|100426483|gb|BY958921.1|BY958921
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18374279|gb|BJ205857.1|BJ205857
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208400702|gb|DC904880.1|DC904880
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18351511|gb|BJ183563.1|BJ183563
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18343480|gb|BJ175518.1|BJ175518
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208399117|gb|DC908226.1|DC908226
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCAACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162264535|gb|FC440857.1|FC440857
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|67718647|gb|BJ968906.1|BJ968906
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162279348|gb|FC455271.1|FC455271
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162278252|gb|FC454591.1|FC454591
EST:     AGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: AGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208361818|gb|DC939040.1|DC939040
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208387862|gb|DC929206.1|DC929206
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208349984|gb|DC910219.1|DC910219
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162277304|gb|FC453734.1|FC453734
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|100417991|gb|BY993284.1|BY993284
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|18331779|gb|BJ163790.1|BJ163790
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|162227859|gb|FC403667.1|FC403667
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208376911|gb|DC906852.1|DC906852
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208378354|gb|DC923025.1|DC923025
EST:     AGGGGAAGAAGGGTGGCCAGAAG-AAAN                         TGTCGACCCNTT-TCCAAGAAGGACT-GTATGATATCAAGGNTCCTAACA-
genomic: AGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|67716290|gb|BJ966550.1|BJ966550
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
EST: gi|208377740|gb|DC940852.1|DC940852
EST:     GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAAT                         TGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC
genomic: GGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 47

CCCTGCTCATCATCATATCTCTTGCTACTCTGTCTGCAGCCATGGCTGTCGGGAAGAACAAGCGGATCTCCAAGGGGAAGAAGGGTGGCAAGAAGAAAATgtaacgtccg ... tggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT
       agttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA