Sequence
atgc intronic sequence ATGC exonic sequencegtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
Basic information
species | Glycine max |
transcript | GLYMA13G34980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 5
gtcagtaacagaatcgttgttggttttgtttggcttttgttattat-tgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
| || |||| || | ||| ||||| || | ||| | || ||| | | | | || | || | |||||||||| || || |||||||| ||||| ||||| || ||||| |||||||||||
---------------gcatgcacttctgttcacctagatcttttacatgctcgtcttag--tttgtgattgatatttattagtgatgctaaacttttgcttaatttgcttgtagACCATAGCAGTGATCCAAGCTGGCCATGGCCTTCTTCAGCTTGGCTCTTGCAAGATC
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
| ||| || |||| | || | | || | | | | ||| |||| || ||||||||| || ||||| |||||||||||||||||||| | || || |||||||||||||||
-----------------------------------gtaaatataatcaaacttcttttggttatatactg---ttcttgatcttaccttaacagtgttttatt---tgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 5
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttat--tttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
|||| | || | | | | || | || |||| || |||||| ||| |||| || ||| | | | || || || | ||||||||||||||||||||||| |||||||| ||| | |||||||||||||||||||||
----gtaaaataaagaacactaatcatatatgag----------aatgttcttgac----tttctt-----gtttctcaagtcacctttgtaatcttttcttattgtacctacagACCATAGCTGTTATTCAAGCCGGACATGGCCTTTTACAACTTGGTTCTTGCAAGATT
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 5
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttcttttt--gttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
||||| | || | | ||| ||||||| | | | ||| | || | | || || ||| ||| || | | || | || ||| | ||||| | || || |||||||||||||||||| ||||||||||| ||||| ||||| ||||| ||||| |||||||||
gtcagaatcacagtagtttgtggttttctattg---ttggtctttgcgttatttgcattattgcttcttttctctgtcc-cttaattttgtcatctttgtatgtcccttgaccagACCATAGCTGTAATTCAAGCTGGCCATGGCCTTCTTCAACTCGGTTCCTGCAAGATT
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05904 (Selaginella moellendorffii), 3'ss of exon 6
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgac-cagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
| ||| | | || |||| ||| |||| | | || | || | | |||| | |||||||||||||| ||||||||||| || || ||||||||||| || || ||||||||
--------------------------------------------gtagctatcc---ggaattctcttt-----cttca--cgggctctaagaaccttgtataccatctcgcagACCATAGCTGTGATTCAAGCTGGGCACGGACTTCTCCAACTAGGATCCTGCAAGATC
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ26828 (Selaginella moellendorffii), 3'ss of exon 6
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgac-cagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
| ||| | | || |||| ||| |||| | | || |||| | | |||| | |||||||||||||| || |||||||| || || ||||||||||| || || ||||||||
--------------------------------------------gtagctatcc---ggaattctcttt-----cttca--cgggctctaagaactttgtataccatctcgcagACCATAGCTGTGATCCAAGCTGGGCACGGACTTCTCCAACTAGGATCCTGCAAGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
tttattttctttttgt CT-rich tract
aaatttattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA