Sequence
atgc intronic sequence ATGC exonic sequencegtaggttatcttgtttttgtttaagcattatgtgtctctggtttattagaagttgtgtgtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G44140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
-------------gtaggttatcttgtttttgtttaagca-ttatgtgtctctggtttattagaagttgtgtg-----taatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
| || | | ||| | | | || || || || | || | || | || | | ||| | | || ||||||||||| || ||||| ||||| || |||||||||||||| |||||| |||||| || || ||||||||||| ||||| ||||| |||||||| || |
tagattgtttggtattggctgttttgcat--atcagatcacttttgcatcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
-------gtaggttatcttgtttttg----tttaagcattatgtgtctctggtttattagaagtt--gtgtgtaatgacaattatgt----gattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
|| || | | | || | ||| | || || | | | ||| || || |||| || | | || |||||||||||| || ||||| ||||| || || || |||||||| |||||| |||||| || || |||||||||| ||||||||| |||||||||| || |
atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G36940.1 (Glycine max), 3'ss of exon 5
--------gtaggttatcttgtttttg----tttaagcattatgtgtctctggtttattaga-----agttgtgtgtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
|| || | | | || | ||| || | || | | | ||| |||| | | | ||| | | |||||||||| || ||||| ||||| || || || |||||||| |||||| |||||| || || ||||||||||| ||||| | | |||||||||| || |
aatttagcatatattgtttgctattggctgttttgcttatcagaccacttttgcatcttaagtattcagttctccctgacctttcttacgaatctttaagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCGGTACGAGAGATTGCACATA
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtaggttatcttg--tttttgtttaagcattatgtgtctctggtttatt---agaagttgtgt-gtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
||| || ||| || || || | | || || | | | || || | |||| | | | | || | |||||| || ||||||||||| || || ||||| ||||||||||| |||||| ||| ||||| || || || || ||||||||| | |||| ||||| || |
aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 6
------gtaggttatcttgtttttgttta------agcattatgtgtctctggttta---ttagaagttgtgtgtaatgacaattatgt--gattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
|| | | | ||| | || ||| | ||| || || || | | | || || | |||| | | | | | | | |||||| || ||||||||||| || || ||||| ||||||||||| |||||| ||| ||||| || || || || ||||||||| | |||| ||||| || |
ttgagggtggttcaccttcctcttagttacactcaaatattgtgccccttcttttcagtttcataaattttaagtaagcaaatctgtctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
upper sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S14_33V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------gtaggttatcttgttt-ttgtttaagcattatgtgtctctggtttattagaagttgtgtgtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
|| | | | |||| || ||| | | | | |||| | | | | ||| | || |||| |||||||| || ||||||||||||||||| || |||| ||| | |||||| |||||||||||| |||| ||||| |||||| ||||| ||||| | |
gtgctttatcttgactcttgcttgatttctttcagctatttacagtttgggaaggggtttgtaagaggctgtggatgttggtgttcattccgcaaggaagaccattgccaagtttggtcgga-tagtgaaatttcctttttttgtgtactccagGGAGAGGCCAAGAGTGCTCAACTCATCGGTGAAGCCATTTCAAACAATCCAGCTTTCATTACCTTGAGAAAGATAGAAGCTAGCAGAGAAATTGCGAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgtctctggtttattagaagttgtgtgtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
tttattagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttatcttgtttttgtttaagcattatgtgtctctggtttattagaagttgtgtgtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA