Sequence
atgc intronic sequence ATGC exonic sequence...acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT4G31750.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
acatacttataatcacatgatagcccttgttcatgaaatttgcaata-agtcgctctgttttgtatggtactaatttgatatttttttttgtttgtc--aaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
| | | | ||||| | | | ||| | | || |||| | |||| | | | | | | |||| |||| ||| | ||| ||||| || || | |||||||| |||||||| | || ||| | |||||||||||||||||||| || ||||| ||||||||||
gctgaatcagaatcagtttctcaaa-tcgtttgtcaggattccaatctaatcgcattacacttca--acaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 4
acatacttataatcacatgatagcccttgttcatgaaatttgca-ataagtcgctctgttttgt-atggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
|||| ||| | | | | ||| |||| | || || | | |||| | | |||| ||||| || | | || | |||||||||||| || ||||||||||||||||||| ||| ||||| || | ||||| ||||| ||||| ||||| |||||||| |
--ctactgctaagctaggagttgattctacggctgatatttcaacattggtgacaccgtttaaccactttcctaacttgatgcattctgcttctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagt-cgctctgttt-tgtatggtactaatttgatat-ttttttttgttt----gtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
|| | | | |||| | | | | | ||| || || || | | | || | |||| ||| |||| | | | ||| ||||| || || | |||||||| |||||||| | || ||| | |||||||||||||| ||||| || ||||| ||||||||||
------ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattt-tttgttatgttttccccatctcggagctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggt-act-aatttgatatttt---tttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
| || | | || | || | ||| ||| | ||| | ||| || | || ||| | || || || | |||| ||| |||||||| || ||||||||||||||||| |||| ||| ||| | ||||| ||||| || |||||||| ||||| ||||||||||
----gtatggcatgttcttgtgcatctactgtgagatagttgttttaa-cctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggt-actaa----tttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
|||| || | | || || |||| || || |||| | || | ||| ||||| ||| | ||| || |||| || | ||| |||||||| || || ||||||||||| ||||||| ||| ||| | | ||| ||||| |||||||| || ||||| ||||||||||
tcatagtttgtacttcttgt--gcttctgttgataaa--ttgct-tcagccttctgaacttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 5
--acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
||||| | | | | | | | | || || | || || ||| | | || ||||||||| | | ||| |||||||| || |||||||||||||| || |||| ||| ||| | | ||| ||||| |||||||| || ||||| ||||||||||
gtttgtacttcttgtgcttctgttgacaaattacttcaaccttctgaatttgaatggtgacttatatatt--ttgctttcccttttttttttcctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGTTTTGTTATGTGGGCTG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
acatacttataatcacatgatagcccttgttcatgaaatttgcaataag-tcgctctgttttgtatggtactaatttgatatttt---tttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
| | || | | || | | | ||| ||| | || ||||| ||| ||| | || || || | |||| | ||| |||||||| || ||||||||||| || || |||| ||| ||| | ||||| ||||| || |||||||| ||||| |||||||| |
----gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
upper sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 5
-acatacttataatcac----atgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
| | | | ||| ||| | ||| | | | | || | || | ||||| | | | | | | || | ||| ||| |||||||| || |||||||||||||| || |||| ||| ||||| || | ||||||||||| ||||| ||||| ||||||||||
gatgaattaaagatcttctctatggagaatttgcttcgtctagtgttcactg-gtttcagtgtttgat----catctgatgaaaacatcttgtaatttcctccagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGCGGCAGCGTATTGAGGATGCTGGAGGGTTTGTGATGTGGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtcgctctgttttgtatggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
tttttttttgtttgtc CT-rich tract
taatttgatatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggtactaatttgatatttttttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - aatcaca
- - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - caataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
