Sequence
atgc intronic sequence ATGC exonic sequence...tgtatgcataaataataaataatacatacatttcacagtcttgtattttcagtttactttgtctctgtaatctgacatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
Basic information
species | Glycine max |
transcript | GLYMA05G24890.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 9
tgtatgcataaataataaataatacatacatttcacagtcttgtattttcagtttactttgtctctgtaatctg-acatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
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-atatctatcgtcttttcagcctgttaaaacaaaattatccactgagtgtttgacacactgtcttttgaatatgcactcattataccttttcttttcttagAATGCTGGAATGCGTCTCTACGGTGGCGCACAATACCATCGGGCAATGGCTGAATTTCGTCTGGTTGTTGGAAGTATTAGATGCCCTCCAATTACTAGGG
upper sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G005848_T01 (Zea mays), 3'ss of exon 9
-tgtatgcataaataa-taaataatacatacatttcacagt-cttgtattttcagtttactttgtctctgtaatctgacatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
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aaccatatactactaccttggctacgaatgtaatataaattacaattatattaagtgcacttttaattcgtttatcaaatctttgaaatgtcctt---tgcagAATGGTGGCATGCGTCTTTATGGTGGTGCACAATACCATCGGGCAATGGCTGAATTTCGTCTGGTAGTTGGTAGTACCAGGTGCCCTCCAATAACTAGGG
upper sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G19720.2 (Arabidopsis thaliana), 3'ss of exon 9
tgtatgcataaataataaataatacatacatttcacagtcttgtattttcagtttactttgtctctgtaatctgacatgctagtttatacacacat-acagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
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tgtgccaaagaataatgtattggaaacaaataaaagaga-tacttcgttggaccttcaagaattatgagagaccataaccagattatctttcattttacagAATGCAGGGATGCGTCTCTATGGGGGTGCACAATATCACCGTGCCATGGCTGAGTTTCGTTTTCTAGTTGGTGCTATCAAATGTCCCCCAATAACGAGGG
upper sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 9
tgtatgcataaataataaataatacatacatttcacagtct-tgtattttcagtttactttgtctctgtaatc--tgacatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
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tctaggcacatactaactctaagctttcctattcattgtttgtttacatttaaatagagtagcatacagaaagagtgtggttttactttttat---tttgtagAATGCGGGGATGCGTCTTTATGGGGGTGCACAATATCATCGTGCAATGGCTGAATTCCGTTTTGTGGTTGGAGGAATCAAATGTCCTCCAATTACAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcagtttactttgtctctgtaatctgacatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
atctgac putative branch site (score: 3)
tagtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatgcataaataataaataatacatacatttcacagtcttgtattttcagtttactttgtctctgtaatctgacatgctagtttatacacacatacagAATGCAGGGATGCGTCTTTATGGTGGTGCACAATATCATCGGGCAATGGGTGAATTTCGTTTTGTGGTTGGAGGAATCAAGTGTCCCCCAATTACTCGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
-gtatgca
- - - -ataaataa
- - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct