Sequence
atgc intronic sequence ATGC exonic sequence...ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctggttattaaaaatattcacgtactctcctttgtttttatgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT5G04540.1 |
| intron # | 10 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 10
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacct-ggttattaaaaatattca--cgtactctcctttgtttttatgt-catagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
| || | | | || | || | || ||| || || | ||| || | | | | | || | | |||| ||| || |||||| | ||||| || ||||| | || || |||||| ||||||||||| ||||||||||| |||||||| ||| | ||||| || ||||||
agaagatgcaagtttgatcgttttcctttg--atgccctt--atctcaatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G449163_T01 (Zea mays), 3'ss of exon 2
-----ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctggttattaaaaatattcacgtactctcctttgtttttatgtc--atagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
|| || |||| || | | || | | | ||| || || | | || ||||||| || | || | || | | |||| | ||||| | || || | ||||| | || || |||||| |||||||||| ||||||||||| ||||||||||||||||| || || |||||||
ccattattctttgatgctct-ctctaaaccacctttactttttttggatatt---atcca--taataaaaat-tttaaatagtgcttattctcctgatgtaaaacagGAAATTGTACATAATTGATGCCCGGCCAAGAGCAAATGCTATAGCAAATGGGGCAAAGGGAGGGGGCTCAGAATCATCTTCTAACTACCATAAATCTGAG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G34510.1 (Glycine max), 3'ss of exon 4
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctggttattaaaaatattcacgtactct-----cctttgtttttatgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
| || ||| | || | || | | || | | | || | || | | | | | | ||| || | | || ||||| ||||| || |||||| | ||||||||||||||||| || ||||| || | |||||| || ||||||||||| ||||| ||||| ||||||||
---gttatgta-tctttttttctgtgcgtgagagg-ggagggggggcgggggtaatttggtgcaatcctctgcattgttttgaaactttttaaattgtatttcagAAAGCTGTATATTGTTGATGCACGGCCTAGGAAAAATGCATTGGCTAATGGTGCCATGGGAGGTGGTTCAGAATCATCATCAAACTATTTTCAATCTGAG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G33040.1 (Glycine max), 3'ss of exon 4
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctggttattaaaaatattcacgtactctcctttgtttttatgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
| | | | | ||| | | |||| | | | || | || ||| | ||| || | | || ||||| ||||| || |||||| | ||||||||||||||||| || ||||| || | |||||| || ||||||||||| ||||| ||||| ||||| ||
ctcaggtagttatgcatctttttttttgtgcatgtgaaaaggggggtaatttggtgcaatcctctgcatttttttgaaacttttttaaattgtatttcagAAAGCTATATATTGTTGATGCACGGCCTAGGAAAAATGCATTGGCTAATGGTGCCATGGGAGGTGGTTCAGAATCATCATCAAACTATTTTCAATCCGAG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0074g00300.t01 (Vitis vinifera), 3'ss of exon 10
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctg-gttattaaaaatattcacgtactctcctttgttttta-tgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
||| || | ||| | || | || || ||| || || ||| | | | | || | | | | | | | | ||||||||| ||||||| |||||||||||||| |||||||| |||||||| ||||||| |||||| |||||||| || ||||| ||||||| || |||||
--ggctgaatgaaatggtcttttaaatgatataaatgtatgtgtgtgcgcacttgtactatgtatattgtgggattaatttaatgaagtgtcacttttttagGAAGCTATATATCGCTGATGCAAGACCTAGAAAAAATGCTTTAGCAAACGGAGCAATGGGAGGTGGCTCAGAGTCCTCTTCTCATTATTTTCAGTCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatacctggttattaaaaatattcacgtactctcctttgtttttatgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
tgttgat putative branch site (score: 4)
tactctcctttgtttt putative PPT
ttattaaaaatattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacctggttattaaaaatattcacgtactctcctttgtttttatgtcatagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- aaaaaaa
- - aaaaata
- - - - - - -ctgctgt
