Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggtatataaaaagaatcctgaacacttaacttattttttaattttatatgtcttgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03190.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 4
------------gtatgtggtatataaaaagaatcctgaacacttaacttattttttaattttatatgtcttgacattattggttgttt--tctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
| | | || | | | | |||| || | | | || || || || | | || || | |||||||||||||| ||||| || || || || || ||| | |||||||||||||||||||||||||| || || ||| | || |||| ||| ||||||
cttatgttaagcttttataacatctttagttgtttcc-aacatttcatattactggtagcattgtacactgtgtaaacaccaaccattccatcatcttcagTGATCAGCTACCTGTGAGTACAAAGTTCGATATGCGTAGTGATCCTGGTGTTGTGAGGAATTATGGCCGCCTCTTGCTGGAAATGGCTTCTGCTGTTCCA
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G008524_T01 (Zea mays), 3'ss of exon 1
--gtatgtggtatataaaaaga--------atcctgaacacttaacttattttttaattttatatgtcttgacatt-attggttgttt--tctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
| | | || || || |||| || | | | || || |||| | ||| || | || || |||| |||||||| || | ||| || || || ||||| |||| |||||||||||||||||||||||||| | | |||||| | || |||| ||| | |||
ttatgttaagctcttatgaaagctttagttatttccaacatttcatattactggtagcattgtatgcttgtgtattcatcaactattccatcatttttagTGATCATCTACATGTGAGTACAAAGTTTGATATGAATAGTGATCCTGGTGTTGTGAGGAATTATGACCACCTTTTGCTGGAAATGGCTTCTGCTATTCAA
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------gtatgtggtatataaaaa----gaat--cctgaac---acttaacttattttttaattttatatgtcttgacattattggttgttttctt-tttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
|| || || | ||| || | | |||| || | ||| || ||| | | | || | || || | | |||||| |||||||||||||||||| || || || |||||||| ||||||||||||| ||||| || |||||||| |||| || ||| | || |||| || |||||||
gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatctccgatttgcttgaaagtgacctcttttacttccccctttgttttattttta-atgtttaatcggtttcttgtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------gtatgtggtatataaaa------agaatcctga---acacttaacttattttttaattttatatgtct-tgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
|| | || | ||| | || ||| | || | ||| || ||| | | | | | | || | ||||| | ||| |||||||||||||| || || || |||||||| ||||||||||||| ||||| || |||||||| |||| || || | || |||| || |||||||
gtattcccataatttgctcccctgtattttaaaacagactttgttaattgttaatacattacattttaaatccctgattttcttgaaagagacctcttttacttccccctttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------------gtatgtggtatataaaaagaatcctgaacacttaac-----ttattttttaattttatatgtcttgacattattgg------ttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
| | || | ||| || || | |||||| || ||||| | || | |||||| || ||| | ||||||||| ||||||||||| || || |||||||| ||||||||||||||||||||||| |||||||| || | ||| || | |||||||| ||| |||||||
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S145_26V6.3 (Physcomitrella patens), 3'ss of exon 7
-----------------gtatgtggtatataaaaagaatcc-tgaacacttaacttattttttaattttatatgtcttgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
|| | | | ||| | | | | | | |||| | | | | ||||| ||| |||| | || | || | |||||| ||||| ||||| ||||| |||||||| ||| | ||||||||||| ||||| | |||||||| || | |||||||||| || ||||||
ctgcatggcattccattgt-tagaacaggtcaaatggttgcatagatatttaagatttgtaatcattttttatttctta----ttccaattttattacaatgcagTGACCAGCTGCCTGTCAGCACGAAATTTGATATGCGGAGTGATCCTGGAGTTGTTCGCAATTACGGTCGTCTGCTACTAGAGATGGTCACTGCTGTTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacttattttttaattttatatgtcttgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
tcttgac putative branch site (score: 3)
ttgttttctttttc putative PPT
tattttttaattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggtatataaaaagaatcctgaacacttaacttattttttaattttatatgtcttgacattattggttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG