Sequence
atgc intronic sequence ATGC exonic sequencegtagcaagccaacctccattgtaactgtggcctgacaataaacatatatactctttgtttctgacagaagtttaactgtttctgtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g68750.1 (Oryza sativa), 3'ss of exon 5
gtagcaa-gccaacctccattgtaactgtggcctgacaataaacatatatactctt--tgtttctgacagaagtttaactgtttctgt--actg-----cagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
|| || || || | ||| | || | || ||| | || | | ||| | ||||||| | || |||| | | |||| |||||| |||||||| |||||||| |||||||| || || || ||| ||||||||| | ||||| | ||||||||||| ||||||||||| ||||
gtgacagcatcagtctatgc-atgtttgttgttgagcacttaatgtattttctactaatatttttaacagaagatcctttggttctactaattatttaccagACCATGAACAAAGTCTTTGAGCATGCTGGAGATCTTGTCAACATCCGAGTTGCACATAATTTAATGCGACTTATTGCTGAAGGCTTTGGAGAGGAGGATG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G146697_T03 (Zea mays), 3'ss of exon 5
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatatactctttgtttctgacagaagtttaactgtttctgtact---gcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
| || | | ||||| | || ||| | | | | | | || || | ||| | | || ||| | | |||| |||||| |||||||| |||||||| |||||||| || || || | |||||| || ||||||||||| | ||||||||||| ||||||||||| ||||
---gtaatcacatgagtattgtc-caacatattgtcaagcatcctttgt--tgcttcttgagagctgaactctttcttcctctattttcttacagACCATGAACAAAGTCTTTGAGCATGCCGGAGATCTTGTCAACATCAGAGTGGCGCACAATCTGATGCGGCTAATTGCTGAAGGCTTTGGAGAGGAGGATG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G031352_T01 (Zea mays), 3'ss of exon 4
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatatactct-ttgtttct----gacagaagtttaactgtttctgtact---gcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
|| | || ||| | || ||| || | | ||| ||| | ||| || || ||| | || |||| |||||| | ||| || |||||||| |||||||| || || || | ||||||||| ||| ||||||| | ||||||||||| |||||||| || || |
-----------gttatcacatgagtattgtcctaaatattgtcatgcatcttttgttgcctcttgagagctgaaccttttcttcctctattctcttacagACCATGAACAGAGTTTTTGAGCATGCTGGAGATCTTGTCAACATCAGAGTGGCACACAATTTGATGCGGCTAATTGCTGAAGGCTTTGGAGATGAGGACG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G35650.1 (Glycine max), 3'ss of exon 4
gtagc-aagccaacctccattgtaactgtggcctgaca----ataaacatatatactctttgtttctgacagaagtttaactgtttctgtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
||| | | || || || | ||| | | ||| | || ||| | | | | | | || || |||||| |||||||||||| || |||||||| |||||||| || |||||||| |||||||||||| ||||||| |||||||||||||||||||||||||||||||
gtaattgaaatagttgcctcaatattattgattttacatttttttgatgcatacattcattgataactaataatatctgg-tattatggttatgcagACCATGAATAAAGTTTTTGAGCATGCTGGAGATCTTGTTAATATTAAGGTGGCACATAATTTGATGCGGTTGATTGCTGAAGGATTTGGAGAGGACGATG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G35240.1 (Glycine max), 3'ss of exon 4
gtagcaagccaacctccattgtaactgt-ggcctgacaataaacatatatactctttgtttctgac--agaagtttaactgtttctgtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
||| | || | | | ||| | | | ||| | | |||| || || | || | || | |||| || |||||| |||||||||||| || |||||||| |||||||| || |||||||| |||||||||||| ||||||| |||||||||||||||||||||||||| ||||
gtaactgaattacttgcctcaatactattgattttacattttttttgcataca-ttcattgataactaataatatctggtgttatggttatgcagACCATGAATAAAGTTTTTGAGCATGCTGGAGATCTTGTTAATATTAAGGTGGCACATAATTTGATGCGGTTGATTGCTGAAGGATTTGGAGAGGATGATG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G20260.1 (Glycine max), 3'ss of exon 4
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatat----actctttgtttctgacagaagtttaactgtttct--gtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
||| | | || | || | | || || | | | || || | || | | |||| | | |||||| ||||||||||||||| |||||||| |||||||| || |||||||| ||||| |||||| | ||||| ||||||| |||||||||||||||||| ||||
gtaatggtgttgctgcatttatgttcttgattttgaattatttatgttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCCCATAATTTAATGCGATTGATTGGTGAAGGATTTGGAGAGGATGATG
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G08320.1 (Glycine max), 3'ss of exon 4
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatat----actctttgtttctgacagaagtttaactgtttct--gtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
||| | || | || | | || || | | | || || | || | | |||| | | |||||| ||||||||||||||| |||||||| |||||||| || |||||||| |||||||||||| | ||||| ||||||| ||||||||||| |||||| ||
gtaatggtgttgttgcttttatgttcttgattttgaattagttattttttgcaaacattcattgataaccaataataccttgttctttgattttgcagACCATGAATAAAGTCTTTGAGCATGCTGGAGATCTTGTGAATATTAAGGTGGCACATAATTTAATGCGATTGATTGGTGAAGGATTTGAAGAGGATGACA
upper sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 5
------gtagcaagccaacctccattgta-actgtggcctgacaataaacatatatactctttgtttctgacaga-agtttaactgtttctgtact-gcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
|| | |||||| | | ||| || | | | | | || || | | || || || || ||| | |||| ||||||||||||||| |||||||| |||||| |||| |||||||| ||||| ||||| ||||||| |||||||| || || || |||||||||||||
gtaattatattgttgccttttccattccagattgtatatgaacgggttgcttgtgtttttttaccttttaatgcttagattttctccttatgtgtttacagACCATGAATAAAGTCTTTGAGCATGCTGGAGATTTGGTCAATATTAAGGTGGCTGATAATTTGATGCGGTTGATTGCGGAGGGGTTCGGAGAGGACGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaacatatatactctttgtttctgacagaagtttaactgtttctgtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
ctgtttct CT-rich tract
atatatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcaagccaacctccattgtaactgtggcctgacaataaacatatatactctttgtttctgacagaagtttaactgtttctgtactgcagATCATGAATAAAGTCTTCGAGCATGCAGGAGATCTGGTAAATATTAAAGTGGCACATAATCTGATGCGTTTGATTGCTGAAGGATTTGGAGAGGACGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA