Sequence
atgc intronic sequence ATGC exonic sequence...gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgcctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G13180.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgc--tcgcctcgcctcttaatttg------actt-acaattc-ttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
|| | || || | || || ||||| | | ||| ||| | ||| || || | | | | |||| |||| | || || | ||||||| |||||||| |||||||| ||||| || |||||||| || ||| | || || ||||| || ||||||||||| |||||| |||||| ||| ||||
gttagtcatcggagcttagccctgcacttttgcataggcatgcctgacactaaaatggatggcaattgcattcagcaggccatgtttcagtgtac-ttgaaaatgtttcatcactgttt-ctcttctttgttgagcgatcatcacactcttatatttatgagaaacttcatgctttgttttcagTGTGAAATGACAGGTGTTGTAGTTGATGTGGGTGATGGGGCTACCCATATCGTTCCGGTTGCTGATGGTTATGTCATTGGGAGCAGTATCAGATCTATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 3
gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgc-ctcgcctcttaatttga---cttacaattc-ttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC---------
|||| | | | | | || ||| | |||| | || || | ||| || || || | | || || | ||||||| |||||||| |||||||| ||||| || |||||||| || || | || || ||||| || ||||||||||| |||||| |||||| ||| ||||
-----------------aaatgcttcat-cgctgtttttctttcttccctgttgagcgatcatcacactcttacatttatgagaaacttcatgctttgttttcagtgtgaaatgacagGTGTTGTAGTTGATGTGGGTGATGGGGCTACCCACATCGTTCCAGTTGCTGATGGTTATGTCATTGGGAGCAGTATCAGATCTATTCCAATTACAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G106513_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------------gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtc-tcgttatgctcgcctcgcctcttaatttgacttacaattc-ttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
| || | | || || || | || | | || || |||||| | || | | ||| | | | | ||| || || | ||||||| |||| ||| |||||||| ||||| || |||||||| || ||| |||| || |||| || ||||||||||| |||||| |||||| ||| ||||
gttagtcatcggagcttagccttgcacttttgcataggctgataggcatggctgacactaaaatggatggcaattgcattcagcaggccatgtttcagtgtacttgaaaatgttttatcacggtttccc-ttctttgttgagcgatcatcacactcttata--tttatgagaaactttatgttttgttttcagTGTGAAATGATAGGTGTTGTAGTTGATGTGGGTGATGGGGCTACCCATATTGTTCCGGTTGTTGATGGTTATGTCATTGGGAGCAGTATCAGATCTATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G092459_T03 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------gctttgtgggatttagcaaatattaaacatgttctct---tgttttttgttctgtctcgttatgc--tcgcctcgcctcttaatttg------actt-acaattc-ttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
|| | ||||| | | ||| ||| | | ||||||| |||| | ||| || || | | | | |||| |||| | || || | ||||||| |||||||| |||||||| ||||| || |||||||| || || | || || ||||| || ||||||||||| |||||| |||||| ||| ||||
gttagtcagcatagcttagccttgttgtttctttagcataggcatgccttacgctaaaatgaatggcaatagcatcgagcaggccatgttttagtgtacttgaaaaatgcttcatcgctgtttttctttcttccctgttgagcgatcatcacactcttacatttatgagaaacttcatgctttgttttcagTGTGAAATGACAGGTGTTGTAGTTGATGTGGGTGATGGGGCTACCCACATCGTTCCAGTTGCTGATGGTTATGTCATTGGGAGCAGTATCAGATCTATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 2
gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgc-ctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
| | | | | | | | ||| | || | || || || ||||||| | | | ||| ||| ||| | |||||||||||||||||||||||||| |||||||| |||||||||||||| || ||||| ||||| ||||||||||| || ||||| || ||||| | |||||||||||||
accat-tagagctatgaagaaattttgtttcttgttttcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 2
gctttgtgggatt-tagcaaatattaaacatgttctcttgttttttgt-tctgtctcgttatgctcgcctcgcctctta-atttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
| | | ||| | ||| || || || | || || || | ||| | | || | | | ||| ||| | ||| |||| ||||| |||||||| || |||||||| ||||||||||||||||| |||||||||||||||||||||| || ||||| || || || | |||||||||||||
--ataacagtaccataggagctatcaag-atattttgtttcttattatatctattttattttaagaatattttcatttatggctgatctgaaatccttcatagTGCGAGATGACTGGAGTTGTAGTGGATGTTGGAGATGGGGCTGCTCATGTTGTACCTGTTGCAGACGGCTATGTTATTGGCAGTAGCATCAAATCGATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 2
-gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgc-ctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
| | | ||| | ||| || | || | || || || |||| || || | | ||| | | ||| | ||||||| ||||| ||||||||||| |||||||| ||||||||||||||||| ||||||||||||| ||||| || || ||||| || || || | |||||||| ||||
tgataacagtaccataggagttatcaat--tttttttttcttattatatctggcttattttatgaatattttcctttaaggctgatctgaaattctttgtagTGCGAGATGACAGGAGTTGTAGTCGATGTTGGAGATGGGGCTGCTCATGTTGTACCCGTTGCGGACGGCTATGTTATTGGTAGTAGCATCAAATCAATTC
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 2
--gcttt---gtgggatttagcaaatat-taaacatgttctcttgttttttgttctgtctcgttatgctcgcctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
| || ||| || ||| |||| | || ||||| | |||| | | | || | || |||| ||| || || |||| || |||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||| || |||||| | || || || ||||
ttgtcttaaagtgtaccttgcttcttatgtaaataatttttcttgctctttgat--gattgattgacc----cttgccttttagattaacctacactttcccttagTGTGAGATGACAGGGGTTGTAGTGGATGTTGGGGATGGGGCTACTCATGTTGTACCTGTTGCAGATGGTTATGTTATTGGGAGCAGCATTAAGTCAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgtctcgttatgctcgcctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
gacttac putative branch site (score: 2)
ttcttctt putative PPT
tcttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgcctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - -gcaaata
- - - - - - - - - - - - aaacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttaca
