Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtatttcttcaagttgatgagatttcagaactataattacacatgttgccagatttcttcttgacttctctatacttaactatgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------gtaaagtatttcttcaagttgatgagat------ttcagaactataattacacatgttgcc--agatttcttcttgac-ttctctatacttaact---atgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
|| || ||| ||||||| |||| ||||| | | | | | | | |||| || ||| || | | || ||| | | | || |||||||| ||||| |||||||||||||||||| | ||||| || || || ||| | || |||||| | | ||||| |||| |||||||||
gtaagtggacgcctttaaaccctgaatgttattacatgtgtagacacacttaaagttgaacagatgtttgattcaggatctccagtgcccctttcattcatgattgctaacagacattatagtttctccactgacacgccaactgctttttcttcagTTTTGACGATCCTGGTCCACATGGAGCAGGCAGATATTCTGATCATATGCTACCTGAAATTGTTAAGAGAGATTGGAGAAAAGGTGCACAG
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G099255_T01 (Zea mays), 3'ss of exon 5
-------------------------------gtaaagtatttctt----caagttgatga-gatttcagaactataat----tacacatgttgccagatttcttcttgacttctctatacttaactatgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
||| || | | | | | |||| | ||| | || || ||| | | || | | | | | | | | || || | | | | || |||||||||||||||||||||||||||| | || || || || || ||| | || |||||| | | |||||| |||||||||| |||
gtaaatgaacatacttacataaagcaacacattaacgtttcccctgatccgaattgaaaaagatatttgatttaaaatgtgctttccttgaaattatgtgtttaaataagaattttgctattgacatgccgaattatctttttcgcagCTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGAGCATATGCTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCGCAG
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G114337_T01 (Zea mays), 3'ss of exon 5
------------------------------gtaaagtatttcttc-----aagttgatgagatttcagaactataat-tacacatgttgccagatttcttcttgac-------ttctctatacttaactatgatag-tgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
| || | | | |||||| |||| | || || || | | | || || | || || | || |||| || || | |||| | | |||| |||||||||||||||||||||||| | || || || ||||| ||||| || |||||| | | |||||| ||||||||||||||
gtaagtgaacatacttacacaaagcaaaacattaactttcccccttgtcagagttgagaagatatttgatttaagatatgctttttttaaattatgtttttttaataagaattttgcttataacatgctgaattatcttttttttccctcagTTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------gtaaagtatttcttcaagttgatgagatttcagaacta--taattacacatgttgccagatttcttct--tgacttctctatacttaactatgatagtg---------ttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
| | | || ||| || | || || || |||| | |||| | ||| | ||| | | | | | || || | | ||||||||| ||||||||||||||||||| ||||| || || || ||||| ||||||||| | | || ||| ||||||| ||||||
gtaaactcaatgttcttattaaaggatgtatccctattgttgcttttgttgtttgggtcaataaaagaattaacattaaacaagtgcactccaatggcccttttggtttaatcttttttgtatattgcaaaatttatcgggatgaaatttctgttttgcatattactgatgcacacccctttcttgttcccagCTTTGAGGATCCTGGTCCACATGGAAATGGCAGATATTCAGAACATATGTTACCGGAAATTGAGATGAGTGACTTTAGAAAGGGCGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagatttcttcttgacttctctatacttaactatgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
acttaac putative branch site (score: 3)
ttttattcttc putative PPT
ttttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtatttcttcaagttgatgagatttcagaactataattacacatgttgccagatttcttcttgacttctctatacttaactatgatagtgttttattcttcagCTTTGATGATCCTGGTCCACATGGAACGGGCAGGCATATGGACCACATGTTGCCGGAAATTCCAAGGGAAGATTTTCGAAAGGGTGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA