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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactatttattttcttctagtgaagtatgggttggtaatatttcctttacacttcaattgagtgtgaatttttgcttaatgcaaattttggaatgtatgctttgggtgttgataatacaatattgattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGTTTGTTGCATGAAGCCAGAAATGTTACCAAGGGTGTCAAGTACGTGTTTC

Basic information

species Glycine max
transcript GLYMA10G38530.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0022g02410.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------gtaaactatttattttcttctagtgaagtatgggttggtaatatttcctttacacttcaattgagtgtgaattt-------ttgcttaatgc---aaattttggaatgt----atgctttgggtgttgataatacaatattgattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGTTTGTTGCATGAAGCCAGAAATGTTACCAAGGGTGTCAAGTACGTGTTTC
                                 |  | |  |||   || |  || |  | | |   ||  |    ||   |||  ||  |||||   | |   |||        || || |      || |||     |||    || | | |  | |  |    |   | |  | | | ||||||||||||||||| ||||  || || |||||  ||||||| ||||  ||| ||||||||||||| |||||||||||||||||| ||||||| || || |
gtaaatcctctttcctttctgtctacttcccttgctatcattttgcattttgttattatattctttctttctttctttcttttttgacaacaattttttttttttttatcttatctgtttgacattagaagtttcattttgttgatatacatcgtctttgaagccaatggtttgcactctgcagGTGGCTCCTACTGAGGGGATGGCTCTCCTGCATATTCATGGGGATATGTGTATGTTGCATGAAGCAAGAAATGTTACCAAGGGTATCAAGTATGTTTTCC
















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|192301621|gb|FG998473.1|FG998473
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTTCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192331818|gb|FK024922.1|FK024922
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         -TGGCTCCTACTGAAAGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192330574|gb|FK022705.1|FK022705
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192331819|gb|FK024923.1|FK024923
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|151404381|gb|EV274191.1|EV274191
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|31311667|gb|CD396870.1|CD396870
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192301620|gb|FG998472.1|FG998472
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTTCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|193482300|gb|FK445733.1|FK445733
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192316313|gb|FK011672.1|FK011672
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192316312|gb|FK011671.1|FK011671
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|37997497|gb|CF809086.1|CF809086
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
EST: gi|192310334|gb|FK002214.1|FK002214
EST:     TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAG                         GTGGTTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT
genomic: TTGGAGGAGAAACAGTGTTTTATGGTCAAAGAAACAAAACTGTGGCTGAGgtaaactatt ... gattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaattttggaatgtatgctttgggtgttgataatacaatattgattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGTTTGTTGCATGAAGCCAGAAATGTTACCAAGGGTGTCAAGTACGTGTTTC
                                         tattgat  putative branch site (score: 3)
                             ttgataatacaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactatttattttcttctagtgaagtatgggttggtaatatttcctttacacttcaattgagtgtgaatttttgcttaatgcaaattttggaatgtatgctttgggtgttgataatacaatattgattttacagGTGGCTCCTACTGAAGGGACAGCCCTACTGCACCTTCATGGAGATAAATGTTTGTTGCATGAAGCCAGAAATGTTACCAAGGGTGTCAAGTACGTGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC