Sequence
atgc intronic sequence ATGC exonic sequence...acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT5G10360.2 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 5
-acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgt-gcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
|| | | || | | || | || ||| | ||| | | || | || || || ||| ||| | | ||| |||||||||||||| ||||||||||||||||||||| | ||||||||||| | ||||||||||||||| | || ||||| ||||||||||||||||| |||||
caccatattatattgtctgcatgtttgtcagttttcaagtcaaaat--atatcttccaggtagctttctgcttacctacctaatggtgttgttgtgttgcagGCAAGAAGGTGAGCAAGGCTCCTAAGATCCAGCGTCTTGTGACTCCCCTCACCCTCCAGAGGAAGCGTGCCAGAATCGCTGACAAGAAGAAGAGGATCGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 5
--acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatg-atttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| || | || | || | ||| | | || || |||| || | | || ||| |||||| || || || ||||||||||||||||||||||||||||||||||||||||||||| ||||| |||| || ||||||||||| || ||||| || | |||||| | ||||| ||
atataatctgtaattttttgaca--tagcctagcatatgcagtcaatttaatggttagtgtagagctgacctatttaccaac-catttatttttttcctgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTCACTCCCCTGACTCTTCAGAGGAAGAGGGCGAGAATCGCCCAGAAGAAGCAAAGAATTGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgat--tgatgatttactaatatatgaggct-----------tccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | | ||| | | | ||| |||| || ||| | ||| | ||| | | | | | ||| | | | | ||||||||||||| |||||||| |||||||||||| |||||||||| || |||||||||||||||||| | |||||||||||||||||||||||||| |||||
-------------ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 4
----acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | || | || || || | | || |||| ||| | | |||| | | | | |||| || |||||||||||||| |||||||| ||||||||||| |||||||||| || |||||||||||||||||| | |||||||| ||||||||||||||||| || |
tactctgcttgttatacgctggatgggtttcttgacaatgagccacagttttctgaagtttt--cgaaccacaacaagctaacctgt-atgtttccttg-gcagGCAAGAAGGTCAGCAAGGCACCTAAGATCCAACGGCTTGTGACACCCTTGACCCTCCAGAGGAAGCGTGCTAGAATCGCTGACAAGAAGAAGAGGATAAC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 5
----acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | | || | || || || | | || |||| | || | | |||| | | | | |||| || |||||||||||||| |||||||| ||||||||||| |||||||||| || |||||||||||||||||| | |||||||| ||||||||||||||||| || |
tactctgcttgttatgcgctggatgggtttcttgacaatgagccacagttttctgaagttttt--gaaccacaacaagctaacctgt-atgtttccttg-gcagGCAAGAAGGTCAGCAAGGCACCTAAGATCCAACGGCTTGTGACACCCTTGACCCTCCAGAGGAAGCGTGCTAGAATCGCTGACAAGAAGAAGAGGATAAC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G048770_T01 (Zea mays), 3'ss of exon 1
--acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatga--tttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC-
| || | | | ||| || | | ||| ||| || | ||| ||| ||| | || || || | | |||||||||||| || |||||||| ||||||||||| ||||||||| || |||||||| ||||||||| |||||||| ||||||||||||||||| |||||
tcttctattagtactctgtgcttgttatat--gttggataggattcatgacaatgagccac-taatttctgaagttttccaagctaacctattttctt-tgcagGCAAGAATGTGAGCAAGGCACCTAAGATCCAATAGCTTGTGACCCC-TTGACCCTTCAGAGGAAGCACGCTAGAATCGCTGACAAGAAGAAGAGGATCGCT
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G583235_T01 (Zea mays), 3'ss of exon 1
acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatga--tttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC-----
| | | || | | || | | ||| ||| || | ||| ||| ||| | || || | || | | |||||||||||| || |||||||| |||||||||||| | | | | || | ||||| | ||| | | |||| || | |||
ctcttctatagtagtctgtgcttgttatatgttggataggattcatgataatgagccac-taatttctgaagttttcaaagctaacctgttttctt-tgcagGCAAGAATGTGAGCAAGGCACCTAAGATCCAGCAGACAAGAAGAAGAGGATCGCT----AAGAAGAAGTTTGAGGTTGAAGGGACAAAGA-GACCACCGCAGCAG
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
--acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
|| ||| | || | | | | | | ||| | | | ||| ||| || || | || | ||| || | |||||| || ||||| ||||| ||||| ||||| ||| | || || |||||| |||| || || |||||| | || ||||||||||| |||||||||||||||||
ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggat-cagttcatattatgaattctagtctcagtaatggatttttggt-tgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
-acaaacaagaagggtaagaaaattagattcacttaaagagataatt---gaaaactgtttatacgattgatgattt-actaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | | | | || || | || ||||| ||| | | | || | |||| | | | | | | ||||| | || ||| || ||||| ||||| ||||||||||| || |||| || ||||| |||||||||| || ||||| || || ||||| || |||||||||||||| ||
tatttatgctgttgtttgatgggtaggacccattgaaggagattatttttggacatgattgtgatgatttctagtctgagttacatatg-----tttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 5
---acaaacaagaagggtaag-aaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| || | || || |||| ||| | | ||| | ||| || | ||||| | ||| | | | | | || || ||||||||| ||| || || ||||| ||||| |||||| | || ||||| |||||| | ||||||||| |||| || ||||| || |||||||||||||| ||
attggttataaaatggttatccaaaaaaagaattggtaaaatggctaactgc--atcttttattctattattaaagccttggggtgcttg--tttaatttgcagGCAAAAAGTGCAGTAAAGCTCCCAAGATACAGAGGTTGGTTACTCCTTTGACCTTGCAGAGGAAGCGAGCCAGGATTGCAGAGAAGAAGAAGAGAATTGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 5
----acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | || | | ||| | ||| || | | || ||| | || | || || |||| | | || || |||| ||||| || || || |||||||| |||||||| ||||| |||||||| || ||||||||| | || || ||||| || |||||||||||||| ||
actgaaattcatgtgatgcttaaaagtattatttcagtattttgctttttaaaa---gacta-aagacagaagattgatatggtttcatcactgtgatcctcagGGAAGAAATGCAGTAAAGCCCCTAAGATTCAGAGGCTGGTGACCCCATTGACTCTGCAGAGGAAGCGTGCAAGGATTGCAGAGAAGAAGAAGAGAATTGC
upper sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------acaaacaagaagggtaagaaaattag--------------attcacttaaagagata-attgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
| | |||| | || | | || | || || | | | || | ||| | |||| | | || | | ||||||||||| |||||||| || ||||||||||||||||||||||| ||||| | ||||||||| | |||| | || ||||||| | | ||||
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcg-tgcgtgctttcagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
tactaat putative branch site (score: 1)
cttccat putative PPT
attgatgatttactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
-caaacaa
- - - - - - - -aagaaaa
- - - - - - - - - - - - - - - acttaaa
- - - - - - - - - - - - - - - - - - - - - - - gaaaact
