Sequence
atgc intronic sequence ATGC exonic sequence...cttattctctttgcctctttctatctttaatgttttcatttgtagttttgtgtacctgatcaatctttatccaaattaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
Basic information
species | Glycine max |
transcript | GLYMA20G03160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------cttattctctttgcctctttctat---ctttaatgttttcatt-tgtagttttgtgtacctgatcaatctt-tatccaaattaatcaagcttaaaatt-----------gttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
| || || | | | | ||||| | |||| | || | | | || | | ||| | || |||| | | || || | |||||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | |||||||| | |||| |||| |||| ||||| |||
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAG---------
upper sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------------cttattctctttgcctctttctatctttaatgttttcatttgtagttttgtgtacct---gatcaatctttatccaaa-ttaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
| | | | || ||| | ||| || || || ||||| ||| || | | |||| | || || | |||| || ||||||||||||||||||||| ||| |||| || |||||||| | ||||| ||| | |||||||| | ||| |||| |||| || || |||||||| |||
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgttt--ctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggtt-ttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAG
upper sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------------cttattctctttgcctctttctatctttaatgttttcatttgtagttttgtgtacct---gatcaatctttatccaaa-ttaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
| | | | || ||| | ||| || || || ||||| ||| || | | |||| | || || | |||| || ||||||||||||||||||||| ||| |||| || |||||||| | ||||| ||| | |||||||| | ||| |||| |||| || || |||
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgttt--ctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggtt-ttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------
upper sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------cttattctctttgcctctttctat---ctttaatgttttcatt-tgtagttttgtgtacctgatcaatctt-tatccaaattaatcaagcttaaaatt-----------gttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
| || || | | | | ||||| | |||| | || | | | || | | ||| | || |||| | | || || | |||||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | |||||||| | |||| |||| |||| ||||| ||||| ||||||
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtgtacctgatcaatctttatccaaattaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
aattaat putative branch site (score: 3)
aaattaatcaagctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttattctctttgcctctttctatctttaatgttttcatttgtagttttgtgtacctgatcaatctttatccaaattaatcaagcttaaaattgttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - ctttgcc
- - - - - - - - - - - - - - - - - - - - - - - - tgtgtac