Sequence
atgc intronic sequence ATGC exonic sequence...taagacttgtaatttcttttctggaaacatctgtacttgttctctttccccatccctgcattttattcattgttaatgatgcacatttaaaatggtttagGTCCGTGCTCTTCAGAGGTTGGGTAGCCGGTTTGAAAATCTTTCTGGACATGACAGATCATGTATCTTATCTGGTCAACATAGAAATGGTCGTTGTGCAT
Basic information
species | Glycine max |
transcript | GLYMA09G35060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G35060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135909_T01 (Zea mays), 3'ss of exon 2
taagacttgtaatttcttttctggaaacatctgtacttgttctctttccccatccctgcattttattc---attgttaatgatgcacatttaaaatggtt----tagGTCCGTGCTCTTCAGAGGTTGGGTAGCCGGTTTGAAAATCTTTCTGGACATGACAGATCATGTATCTTATCTGGTCAACATAGAAATGGTCGTTGTGCAT
| ||| | || || | | | | || || | ||| | ||| | | | | | || |||||| | ||||| || |||||||| ||| ||||||||||| | ||||| ||||| ||||| || || |||||||||| ||||||| || ||| |
-------------------------gtaagctggatttcaactttatttc-agccttggttattacctgaaagaattataggtttataccttttgctgtcttaatagGTCAGAGCTCTACAAAGGTTGGGCAGCAGGTTTGAAAATTTATCTGGTCATGAGAGATCCTGCATACTATCTGGTCAGCATAGAACAGGAAATTGCAACT
upper sequence: GLYMA09G35060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0087g00420.t01 (Vitis vinifera), 3'ss of exon 2
----taagacttgtaatttcttttctggaaacatctgtacttgttctctttccccatccctgcattttattcattgttaatgatgcacatttaaaatggtttagGTCCGTGCTCTTCAGAGGTTGGGTAGCCGGTTTGAAAATCTTTCTGGACATGACAGATCATGTATCTTATCTGGTCAACATAGAAATGGTCGTTGTGCAT
|| || || | | |||| | || ||| | | | | || | ||||| ||| || || |||| ||||||| |||| ||||||||||||||| | || || || ||||| || || ||||||||||| ||||| ||||||| ||| ||||||||||||| ||||||||| |||
atcttacagaagacaagtttctcattttaaaccctttctctggttttgatg---taatcatgtaaccgattcaa-attagcgactcatatttcaaatggtgcagGTTCGTGCTCTTCAGAGGCTAGGCAGTCGTTTTGAGAACCTGTCTGGACATGAGAGATCTTGTATCTCATCAGGTCAACATAGAACAGGTCGTTGTACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccccatccctgcattttattcattgttaatgatgcacatttaaaatggtttagGTCCGTGCTCTTCAGAGGTTGGGTAGCCGGTTTGAAAATCTTTCTGGACATGACAGATCATGTATCTTATCTGGTCAACATAGAAATGGTCGTTGTGCAT
tgttaat putative branch site (score: 3)
attttattcattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagacttgtaatttcttttctggaaacatctgtacttgttctctttccccatccctgcattttattcattgttaatgatgcacatttaaaatggtttagGTCCGTGCTCTTCAGAGGTTGGGTAGCCGGTTTGAAAATCTTTCTGGACATGACAGATCATGTATCTTATCTGGTCAACATAGAAATGGTCGTTGTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - -tttctgg
- - - - - - - - - - - - - - -tctgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcac