Sequence
atgc intronic sequence ATGC exonic sequence...aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
Basic information
species | Glycine max |
transcript | GLYMA15G06380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
aatgtaatactc-ttgatgccgatttgtatacggtc-tacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttc--tgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
|| || || || | | | || | | | |||| || | | | || | | || | ||| | ||| || | || ||||||| ||||| || || || || ||||| ||||||||||| ||||| |||||||| ||||||||||| | |||||||||||||| | || || ||||| |
--agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggc-atagagcactat-taatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g31190.1 (Oryza sativa), 3'ss of exon 1
---aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
| ||||| || | | || || || || | | | || || | | || || | | | ||| ||| | ||| ||||| |||| ||||| || || |||||||| || || || || |||||||| ||||| || |||||||||||||| || || ||||||||||| |
gtacttataataatccttcttttttttggttgggggggggtgggtcttgtttta--tgctttcgtgattcttacgagatgaattatgttgactgttttt-cagTTGGAAACGGATAAAGAAGCTGGGGGCAACAAAGGGGTTTCTGAGAAACAGATTCGTCTGAAAATATTTTCACCAAATGTCCTAGACATCACCTTGGTTG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
| | || | | | | || | | || || | || ||| ||| | | | |||| | | ||||||| ||||| || | || |||||||| ||||||||||| || || | |||||| ||| ||||||||||||| |||||||||||| | || || ||||| |
tgtttggtattttgtttcacttcttttctttagttagtgtgggcttgagttgccattagtgctccacagaccattgttaaaagactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 1
aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtat--atcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
||| ||| | | || | | || || || || ||| | | | | | | ||| | | ||||||||||||| ||| | || |||||||| ||||||||||| || || | |||||| || ||||||| ||||| || ||||| ||| | || || || || |
--tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgagattagtgctgcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
--aatgtaatactcttgatgccgatttgtatac-ggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
| | | || ||| | ||||||| || | || || | || | | || | |||| || | ||| |||||||| || ||||||||||| || | ||||||||||| ||||| ||||||||||| | ||||| || || |||||||| ||||||||||| | || |
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctt---tccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
aatgtaatactcttgatgc-cgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgac-tagtatatcttcactcacttttt---ctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
| || | ||| ||| || | ||| | | | | | || | ||| | || || || ||||| | |||||||||||||||| ||||| || |||||| || | || || ||||||||||||||||| ||||||||||| |||||| | | || || | || |
-----gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
cactcac putative branch site (score: 2)
tcttcactcacttttt CT-rich tract
tagtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtaatactcttgatgccgatttgtatacggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - ctacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcac