Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaataactaaatcatacacaacttgcaagactttagttgttggtgttttgctaatggcgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
Basic information
species | Glycine max |
transcript | GLYMA03G03200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 3
------------gtaaaaataac-taaatcatacacaacttgcaagactttagttgttggt------------gttttgctaatgg----cgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
||| ||| | | | | || | | | | | | || || |||||| ||| ||| | | | |||||| | |||| |||| ||||| || ||||||||||| ||||| |||||||| ||||| | ||||| |||||||| || || |||||||| || || ||
gtaatacttctaataacgccaacgtgcagcgtctcgcttttattacagtcttgcttttagtctgtgtggcacagttttggtaacatgtttcgtggatcctgtacagGTACGTTATTTTGGGAGATGGCTGCCAAATGGAGGGTATTGCTAATGAAGCTTGCTCCTTGGCTGGACACTGGGGTCTTGGCAAGCTGATTGCTTTCTAC
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaaaat--aactaaatcatacacaacttgcaagactttagttgttgg--tgttttgctaatggc-gtttgttttatgc-agGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
|||| | | ||| ||| || |||| | | | || |||| ||| || | | | || ||| |||||| | ||||| || ||||||||||| ||||| || ||| ||||||||| ||||| || ||||| ||||||||||| || ||||| || || || ||
gtaagattttgactccttca-acggcacttttattgttatctttcttggattgtgatgttgtaaactgactgctttggattagGTATTCGATTCTTGGAGATGGTTGTCAGATGGAAGGGATTTCAAATGAAGTTTGCTCTCTAGCTGGTCACTGGGGACTTGGAAAGCTAATCGCTTTCTAC
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaaaataactaaatcatacacaacttgcaagactttagttgttggt-gttttgctaatggcgtt--tgtttt---------atgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
|||| | || ||| |||| | ||| ||| |||| | | | || |||| | | |||||| | || ||||| || || || ||||||||||| |||||||| ||| | |||||||| ||||| || |||||||| |||||||| || ||||| || || || ||
gtaata-tatataacccatagttatgttgtcgttcttggtttgtatatagctctgataatagaaatactgtttttgattgattgtctagATATGCGATCCTTGGAGATGGTTGTCAGATGGAGGGTATTTCTAATGAAGCTTGCTCTCTAGCTGGCCATTGGGGACTTGGAAAGCTCATTGCTTTCTAC
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtaaaaataactaaatca---tacacaacttgcaagactttagttgttggtgttttgctaatggcgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
|| | ||| ||| || |||| | | | ||| ||||| || ||| | || | || || | ||||||| || || |||||||| ||||||||||| |||||| ||||||||| || || |||||||| |||||||| || ||||||||||| |||||||||
gtaaatcctcattcttggtgttcttgttctgtttcctatctcaatgtatacaa-tcatttggccttacttgtt--tggttttttgatattgattattct---tagGTATGTGATACTTGGTGATGGATGTCAAATGGAAGGAATTTCAAATGAAGTTTGTTCCCTTGCTGGGCACTGGGGGCTTGGGAAGCTGATTGCATTTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacttgcaagactttagttgttggtgttttgctaatggcgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
tgctaat putative branch site (score: 2)
tttgtttt putative PPT
tttgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaataactaaatcatacacaacttgcaagactttagttgttggtgttttgctaatggcgtttgttttatgcagGTATGCTATTCTGGGTGATGGTTGTCAAATGGAGGGAATTGCAAATGAAGCATGCTCACTTGCTGGCCACTGGGGACTGGGGAAGCTGATAGCATTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT