Sequence
atgc intronic sequence ATGC exonic sequencegtatataattaaatgtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
Basic information
species | Glycine max |
transcript | GLYMA02G05160.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatataattaaatg-tatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
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gtaaacgaataaaagacatctcatgaatcatctttt-cggtgttggattcttcatcttttgatgaaaaca-atgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatataattaaatgtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
||| || | | | ||| | | ||| | || | | | | |||||| | || | ||| || || | |||||||||||||||| || ||||| |||||||| |||| || | ||||| |||||||| ||||| |||||||| ||||| || ||||| || || || | |
gtacgtagattagtatatatacc----cttgttgcagatttctaatgttaat-gttaatgctaatgttgatgatg--tgagagtgcagAATGTGAAGGCGGTGTTTGACGCAGCCATCCGAGTGGTGTTGCAACCGCCAAAGCAGAAGAAGAAGAAGAGCAAAGCGCAGAAGGCATGCTCCATTCTAT
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------gtata-taattaaatgtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgaccttta-ttgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT---
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gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGT-CAAAGTCTA--AGGTCTGCTCCATATTGTGAA
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
---------gtat-ataattaaatgtatt-tcctttttcttttcacacaatggttaagtta-attggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT--
|| | ||| | | ||| | | | | | |||| | | | | || | || | || ||||||||||||||| ||||| ||||||||||| || | || || ||||| ||||| ||||| ||||| ||||| | || ||||||| ||| ||| | |
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAA---AAAAACAAAAGAACTGTGTCATACTCTGA
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtatataattaaat--gtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatat-ttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT---
|| | || | ||| | | | || || | | ||| || | || | || | ||| | |||||||||||||||| ||||| |||||||| ||||||| || || ||||| ||||| ||||| ||||| ||||| | || |||||| ||| || | |
tttctgtaggtgggaacttgcaccaagattatgtcaactatgtagtgcactgtgtcaattatttttttgtttgatggcgatttattgtattctattgcagAATGTGAAAGCAGTTTTTGATGCCGCCATAAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAGAAG---CAAAAGAACTGTGTCATTCTCTAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
atttgac putative branch site (score: 4)
cctttatt CT-rich tract
ttaattggtagtcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataattaaatgtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG