Sequence
atgc intronic sequence ATGC exonic sequence...agaagtttttcgttgctctttacacatgtgtcttttaattaatttacctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
Basic information
species | Glycine max |
transcript | GLYMA15G07760.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 6
-----agaagtttttcgttgctctt----tacacatgtgtcttttaattaatttacctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
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gtaacttgattatctcgattcttttaggcttttcttgggacatgataccagcttactttaggagctg-tgtggtgctcgaattttatttaaatttcttttttttt-cagGCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 2
------------------------------------------agaagtttttcgttgctctttacacatgtgtcttttaattaatttacctaaataatttctgtagt--tgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
| | || || ||||| | | | | || || | | | | | | | | || | |||||| | | | ||||| |||||||||||||||||||| |||||| ||||||| || || ||||||||||||| || |||||||| |||||||||||||||||||||
gtaacttgcttcttgtatctcagtaatttacttctttctctgcttattcatttttttttctttgtaga-gcgctgcggaactattcattccagtttggtgccatgatcatgagctacctaattgatttctaaatgtgtacacagGCGTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGGGAGCGCATGCAGCCCAAAATGGGCAAAATGGATATAGATTATCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 5
--------------------------agaagtttttcgttgctct--ttacacatgtgtcttttaattaatttac--ctaaataatttctgt-agtt--gctgttt-----ttaattgtcatat-gttatct-------catgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
| | | | | |||| ||| || | | || | | || | || ||| | | |||| | | | | || | | || | | ||| | |||||||||||||||||||||||||| |||||| ||||||| || || | ||||| ||||| || || ||||| |||||||||||||||||||||
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
agaagtttttcgttgctctttacacatgtgtcttttaattaatttacctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
| ||| ||| || || | | || | |||||| |||| || ||||| | | || | ||| ||| ||||||| ||||||||||| ||| ||||||| |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || |||
-----gtaaaagttattctctatcaatataaggtgcaagtcg-----ctaaatg-cttctactgtca-----gctaattcttgtgtggt-tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
upper sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 6
-agaagtttttcgttgctctttacacat-gtgtcttttaattaatttacctaaataatttctgtagttgc-tgtttttaattgtcatatgttatctcatg-cagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
| ||| | | | | || | ||||| | | || || ||| ||| | | ||| |||||| | ||| |||| | |||||||||||||| || || || || |||||||| || |||||||| ||||| ||||| ||||| |||||||| ||||| ||||||||||||
tctatatttggaaattcaatctggactcagcatctttagacataacggccc---tactttgtgttatgccatgtatttaat-attttatcttatgggctatcagGCTTATATTGAAAAGGAAGACAGCAAGAAGCTTAAGCAAAAGCAGAGGGAAAAGATGCAGCCAAAGATGGGGAAGATGGACATAGATTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
ttttaat putative branch site (score: 3)
ttatctc putative PPT
tttttaattgtcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagtttttcgttgctctttacacatgtgtcttttaattaatttacctaaataatttctgtagttgctgtttttaattgtcatatgttatctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
- - - - - -gttgctc
- - - - - - - - - - - -acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgt