Sequence
atgc intronic sequence ATGC exonic sequencegtatgtattttagttaaaatgttcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
Basic information
species | Glycine max |
transcript | GLYMA10G37730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 4
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
gtatgtattttagttaaaatgt-tcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
|| | | | || || | |||| | | | | || || || | || ||||| || || || | ||| |||||| | || | ||| ||| ||||| || || ||||||||||| |||||||||||||||| || ||||||||||| || || | |||||||| || || | |||
--ataactctaaactatcatctgtcttgactagctaaatgtt--ttattgcacttggtcatt-----atttgtttccttatttgaattgttc--------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 2
gtatgtattttagttaaaatgttcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
| || | || | || | || | || ||| ||| || | | ||| |||| ||||| || | || | | | || ||||||| ||||| |||||||| ||| |||| ||||||||||| || | |||||||| || || | ||| ||||| |||||||| ||||
atccactttccatttgagcaattttcaaat-catgcttaagt-ttccgcaaacctttgctttgtataccct-atcttgata-------------ccatcatctgtattactattagTGATAGTGGTGAAATGTGCGCAATGAAAGAGGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAGAGTGCAAAGCAATTGGGGCAG
upper sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtattttagttaaaatgttcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
||| | | || | |||| | ||| | |||| | | | | | || ||||| || | | ||| | || || || |||||||||||||| |||||||||||| |||||||||| || || |||||||||||| | ||||| | ||||||||| || || || |||
--------ctta--tgatatctaagcaattgatttgcgactccatgtttttaaatgttgatcttttac-tggat-----ttgtgcatatctgattttatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
tcttaat putative branch site (score: 3)
tgtttgtctctttt putative PPT
tttgtttaaaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtattttagttaaaatgttcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA