Sequence
atgc intronic sequence ATGC exonic sequence...gttcatttctattagactgattattttaagacttaattttatttttcatttatgctttacaagcaactaatttgtatgtgaatgtgctcactgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
Basic information
species | Glycine max |
transcript | GLYMA19G43270.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
gttcatttctattagactgattattttaagacttaattttatttttcatttatgctttacaagcaactaatttgtatgtgaatgtgctcactgt-gctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
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--------gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
upper sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------------------------------------gttcatttctattagactgattattttaagacttaattttat--ttttcatttatgctt---tacaagcaacta-----atttgtatgtgaatgtgctcactgtgct-cagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
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gtactattctcttgtcgagttgtaatgatatatatgttattttctctttttagtttttagtagctaattcaacttacacttttgcattgtggtatcgagtagtacttgaatattatcaaatagaaatattttcttatgaattttgtaattgtgtgacagCGTTTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAA
upper sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
gttcatttctattagactg-attattttaagacttaattttatttttcattt-atgctttacaagcaactaatttgtatgtgaatgtgctcactgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
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gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaattt--aactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttatgctttacaagcaactaatttgtatgtgaatgtgctcactgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
tgctcac putative branch site (score: 2)
taatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatttctattagactgattattttaagacttaattttatttttcatttatgctttacaagcaactaatttgtatgtgaatgtgctcactgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgtg