Sequence
atgc intronic sequence ATGC exonic sequencegttggctgcattcattcttcatgttgactatttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
------------gttggctgcattcattcttcatgttgactat--ttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
| || || | | || || ||||| | | |||| || ||| | ||| || | | | | || || ||| |||| |||||||| | ||||||||||| | | ||||| || |||||||||||||| || ||||||||||| || |||||| |||| ||||| || |
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatggctgg-----aatgccttgat--cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
------------gttggctgcattcattcttcatgttgacta---tttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
|| || | | || || ||||| | ||||| | || ||| | ||| || | | | | || || ||| |||| |||||||| | ||||||||||| | | ||||| || |||||||||||||| || ||||||||||| || |||||| |||| ||||| || |
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctgg-----aatgccttgat--cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
--------------------------------gttg--gctgcattcattct--tcatgttgactatttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
||| ||||| | || | || || || || | || | || ||| | | ||| |||||| |||| |||| |||||||| | || |||||||| | ||||||| || |||||||||||||| || || |||||||| |||||||| | |||||||| ||||
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgcttttt--aatttaataacctgtgtccatt-tctgga--gcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
-----gttggctgcattcattcttcatgttgactatttttca--gttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
| | | | || | | || | | || | || ||| | | | ||| || |||| |||| |||||||| | || |||||||| | | || || || |||||||||||||| || || ||||||||||||||||| | || ||||| || |
gtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttattga---gcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
---------------gttggctgcattcattcttcatgttg--actatttttcagtta--attataggaaaccgatagattat-tattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
| || | ||| || ||||| | | | ||| ||| | | | |||| | | | || | |||| | || |||||||| | ||||||||||| | ||||||| || |||||||||||||| || || |||||||| |||||||| | |||||||| ||||
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
---gttggctgcattcattcttcatgttgactatttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
| | || || || || || |||| | || | | || || || |||| || | ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || |||||||||||||| || ||||| ||||||||||| ||||
gtaagagtttaaatctatctatcgagtacac-atttat--atttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 26
gttggctgcattcattcttcatgttgactatttttcag--ttaattataggaaaccgatagatt----attattattatctg-----gaatg-------cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
|| | || || || | || | |||||| |||| || | ||| || | | | ||| |||| ||||| ||||| || || || || ||| |||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| || ||||| || |||||||| || |
gtaaagttcaaatatactacccctttaatattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacagATCGAGAAACACGAACTTGTTGAAATGAGACGTGTGGCTGCTTATATCTACAAGAAAGCGGGCAGATGGAAGCAATCAATTGCATTATCAAAGAAAGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gttggctgcattcattcttcatgt-tgactatttttcagt-taattataggaaaccgatagatta--------ttattattatctgga-atgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
|| | | | | ||||| | || | | |||||| | | || || | | | | | |||| || || ||| || ||||||||| || || |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| || |
gtggagtataat--ttctttaggtgcaattgtttttctttgtggttctatgca-ctggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
agttaat putative branch site (score: 4)
atagattattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggctgcattcattcttcatgttgactatttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG