Sequence
atgc intronic sequence ATGC exonic sequencegtctgatttgtgtacccatttggtttgattcactttctagttgtgattttggttttcttgggtttgcatggatattgtttgatgtgttttgttttgggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
Basic information
species | Glycine max |
transcript | GLYMA08G43200.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctgatttgtgtacccatttggtttgattcactttctagttgtgattttggttttcttgggtttgcatggatattgtttgatg--tgttttgttttgggttta---gGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
| || || | |||| ||||| | || || | |||||| | || ||| | | |||||| | || | || |||| || ||| || || |||||||| ||||||||||| ||||||||||| ||||| || ||||||||||||||||| |||||||||||||| || || || ||||| |
---agtttcaggttcacattg---ttgatatttacttgagctgaagaatcaattttct--gtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
upper sequence: GLYMA08G43200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctgatttgtgtacccatttggtttgattcactttcta-gttgtgattttggttttcttgggttt----gcatgg---atattgtt--tgatgtgttttgttttg--ggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
| ||| | | | | |||||| || || |||| | | || ||| || | ||| | |||||| | | | ||| | ||| | | ||||| || || ||||||||||||||| |||||||||| || |||||||| ||| | |||||||| ||||||||||||||||| |||||||| | || | |
--gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
upper sequence: GLYMA08G43200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 3'ss of exon 3
-----gtctgatttgtgtacccatttggttt-------gattcactttctagttgtgattttggttttc--ttgggtttgc-----------atggatattgtttgatgtgttt--tgttttgggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
| | || ||| | ||| |||| ||| | | | ||| | ||| |||||| ||| | ||| ||| | | | || ||||| | || | |||||||||| || ||||||| |||||||| |||||||||||||| |||||||| |||||||| || |||||||||||||| ||||| |||||||| ||||
gtcagatattgattctgttcatctttagtttctttcctagttcgttgacaaattgggttttgggtttttcattgtggctgccaactggggttgtgggtttctctcaatttgtttgttaattcctgaccagGTGATTCCGGGTGAGTATGGGTTCATTGCCCAGCTGAATGAGGGCCGCCACCTGAAGAAGAGGCCCACTGAGTTCCGTGTGGATAAAGTCCTCCAGCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttttcttgggtttgcatggatattgtttgatgtgttttgttttgggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
gtttgat putative branch site (score: 5)
ttttgtttt putative PPT
atattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgatttgtgtacccatttggtttgattcactttctagttgtgattttggttttcttgggtttgcatggatattgtttgatgtgttttgttttgggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA