Sequence
atgc intronic sequence ATGC exonic sequencegtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
Basic information
species | Glycine max |
transcript | GLYMA10G16320.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
gtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
| | || | ||||||| ||| || || | | || | || || | | | || || | | | || |||||||||||||||||||||| |||||||| || || | | ||||| |||| || || ||||||||||||||||| |||||||| |||||||||||
---------gtatgctgtgaccaccagtattttttt--acacttacaaactg----ttatgtcctgaagcatatttaacagtggcttttgctgtcttct-ttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G827205_T02 (Zea mays), 3'ss of exon 2
---------------------------------gtaagttatgagtatggtaaatctgagtatttgtt-ttgactctaatatcttggaactga-----tatcaatagaagaaaggagcattgttatgaattatttttggttt--------tgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
|| || || | | ||||||| | | || || |||| || ||| | | | ||| || | || |||||| | | ||||||||||||||||||| ||||||||||| | | ||| || || |||| || || |||||||| |||||||| |||||||| |||||||||||
gtatgcagtgacgagcagtattttttaacatttacaaactactccctccgttcttttt--tatttgtcgccggcgaaaaaattcgagaacggaggtagtatgtcttatgtcctgaaacatgtttcacagttgtttttgttgtcttcttgttgcagTGGCTTGTTGAATATAATGCAGCATTGACATCCATCTGCTTTATGATTCTTCTTGGATTTGTTGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
|||| | || | || ||| | |||| | | ||| | | || | | | || | || || | ||||||||||||| || || ||||||||| |||| | ||||| ||||||| |||| |||||||| ||||||||||||||||| || ||||||||
----------------gtaagtgtgcattaacgtcttgttttattaatctctg--tggttattctcattatcaatgtttgtgagtctggctgatgatt--ctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G57220.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagt-------tatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatt--tttggttt----------tgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
|||||| | | | | || ||| |||| ||| | | | | | || | || || | | | | | | | | |||| | ||| | ||||||||||||| || || ||||||||| | |||| ||||| ||||||| | |||| |||||||| ||||| ||||||||||| || ||||||||
gtaagtgtcctggtctcaaaagctcaagcttgatcatttattt--attgtga-actatgaacttggtagctcttggctcatttactttgaatgcaatttatcaatctggctaaatgactcggtgcagTGGCTTGTGGAGTATAATGCAGCACTGGCGTCTATTTGCTTCATGATATTGCTTGGATTTGTAGATGACGTCCTTGATGTGCCTTGGAGAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 2
gtaagttatgagtatggtaaatctgagt---atttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
| | ||| | ||| | || || | | ||||| | | | | | | | | | |||| | | |||| | || || | |||||||||||||||| ||||||||||| ||||| | ||| || |||||||| ||||| |||||||| |||||||| |||||| | |||||||||||
-----atttaagttagctaagccctaggttagttaggtctgactttgaagacattttcttcttttaacttttagaattaa--aatgttg---actacttc-attcatgcagTGGCTTGTTGAGTACAATGCAGCCTTAGCATCCATCTGCTTCATGACCCTGCTTGGATTTGTAGATGATGTTCTTGATATTCCATGGAGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
aactgat putative branch site (score: 3)
ttatgaattatttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA