Sequence
atgc intronic sequence ATGC exonic sequencegtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
Basic information
species | Glycine max |
transcript | GLYMA20G38770.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 8
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatcttt-ttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
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----gtttgccactttgtctcctatatttcatataatattcatatctg---tctactagttatgacattagttctatgtccaaacttctc---tcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATACACTAGTATTCCTTCAC
upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G017835_T02 (Zea mays), 3'ss of exon 7
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatcttt-ttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
|| || | | | || |||| | | | ||| | ||| | || | | | | | | ||| |||| ||| ||| | || ||||||||| || ||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| | || || ||||| || |
----gtttgccactttgtctcctatatttcatataatattcatatctg---tctactagttatgacattagttctatgtccaaacttctc---tcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA-----------------
upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 8
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggtttt--cttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
| | | |||||| || | | | | | ||| || | | | | | | || | | ||| ||| | ||| | |||||| || ||| |||| || |||| ||||||||||| |||||||||||||| ||||| |||||||| ||||| | ||||| ||||| | || |||||
----------------------gtaatatattttctactgttacctaatataatttgttttatactcgctcttaccttttgttgaatctctc---tcttcttaatttttatagAGGGACAGTTAGATACGCAAGTGCACATGCTCATTTAGGGAGAACTGCTAGCAGAAGGGATGATCTGGAATCATTAGCATATACACTGATCTTTCTTCAC
upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 8
--gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
| ||| | | | | | | | || || ||| || |||||||| || | | || | | || || | || || || |||||||| |||||||||||||||||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| | |||||||||
gtgaattgatgttgtgtttgtgggccatgctttgtgatttttgaactta--------ttttttttaatccttcattcttgattatttttactgt------ttgcttcatccagGGGAACTGTGAGATATGCTAGTGTTCATGCTCACTTGGGAAGAACTGCCAGCAGAAGAGACGATCTAGAGTCTCTTGCATATACACTCATCTTCCTTCAT
upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 6
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
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-----------------------------------------------------------gtatcactcttgtgtatctgtggatcgggctaagttttagttgtgt-ttcagGGGAACTGTTCGGTACGCAAGTGTCCATGCGCACCTGGGTAGAACCGGTAGTAGAAGGGACGATCTGGAATCTCTTGCCTACACGCTGATATTCTTACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttttaatggttttcttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
ttttaat putative branch site (score: 3)
ccttatctttttat putative PPT
ttatctttttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG