Sequence
atgc intronic sequence ATGC exonic sequence...agctggtctgacacattttggtgacagttgtgctatccttctctctaatagaacaagcaaaaaggatttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 1
agctggtctgacacattttggtgacagttgtgctatccttctctctaatagaacaagcaaaaaggat-ttgttgactgaa--------ttatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
|| || | |||| | || || || |||| | || | ||| || | | |||||||| | |||||| || ||||||||||||||| || ||| | |||||||||||||| |||||||| ||| | ||||| | |||| || ||| | || | ||| || |||||||||||||
----aatcatgtgaatct--gtgatacttacact-tctttctatg-gatggtgcaaacactgcctgtacttctgactgaaatgaaatatcatcttttggt-tttggcagATGACAACGGCCATTTCCATTGAAGATGTTCGTAGGGAGGTCAAGATTTTGAAAGCCCTATCAGGGCACGATAATCTCGTCAGATTCTATGATGCATGTG
upper sequence: AT2G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G05750.1 (Glycine max), 3'ss of exon 1
agctggtctgacacattttggtga--cagttgtgctatccttctctctaataga-acaagcaaaaaggat-ttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
| || || | || | | ||| | | | || | || ||| | ||| | || |||| ||| | || | |||||||| || ||||| |||||||||||||||||||| ||||||||| || | ||| | ||||||| || ||| || | |||||| | ||||||| | ||
----gaaatggcataaattaggaaatttgttatctaaatttactgttcaaaagatgttaataaacactatactgtttctcatcttaataaattttattcatcagATGACCACTGCAATAGCAATTGAAGATGTTCGCAGAGAGGTGAAGATATTAAAAGCTCTATCTGGCCATAAACATCTCGTCAAATTTCATGATGCTTTTG
upper sequence: AT2G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G02340.1 (Glycine max), 3'ss of exon 2
agctggtctgacacattttggtga--cagttgtgctatccttctctctaataga-acaagcaaaaaggat-ttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
| || || | || | | ||| | | || | || ||| | | ||| | || ||||| ||| | || | |||||||| || ||||| ||||||||||||||||||| ||||||||| || | ||| | ||||||| || ||| || | ||||| | | ||||||| | ||
----gaaatggcataaattaggaaatttgttatctaaattaacttttcaacagatgctaataaacactatattgtttctcttcttaataaattttattcatcagATGACCACTGCAATAGCAATTGAAGATGTTCGCAAAGAGGTGAAGATATTAAAAGCTCTATCTGGCCATAAACATCTCATCAAGTTTCATGATGCTTTTG
upper sequence: AT2G46700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 1
agctggtctgacacattttggtgacagttgtgctatccttctctcta-atagaacaagcaaaaaggatttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
|| | || | | |||| | | | ||| ||| | || | ||| || | | | | ||| | ||| | ||| ||||||||||||||||| ||||||||||||||||| || ||||| ||| || |||| | |||| || || || || |||||| ||||||||||||||
agtggacctca-aaatttagaagctatgaactatattcttattattatgtttgacatatcaactatgtagttacagtatcttaacaatcttaaattgacagATGACAACAGCAATAGCAATTGAAGATGTTCGTAGAGAGGTAAAGATATTGAAGGCTCTATCAGGGCATGCGCATCTAGTCAAATTTTATGATGCATGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatagaacaagcaaaaaggatttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
tgttgac putative branch site (score: 3)
tctttctgt putative PPT
aattatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctggtctgacacattttggtgacagttgtgctatccttctctctaatagaacaagcaaaaaggatttgttgactgaattatctttctgtacttggcagATGACAACAGCAATTGCAATTGAAGATGTTCGCAGGGAGGTGAAGTTACTGAAATCATTATCTGGACACAAATATTTAATCAAATATTATGATGCATGTG
- - - -ctgacac
- - - - - - - attttgg
- - - - - - - - - - - - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - - - - - - - - -agaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatttgt