Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattttttttctgtattgggttgatgcaaattttttactgtgttccacacttgttaatcataaactttcagTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45100.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G150362_T01 (Zea mays), 3'ss of exon 1
--------------------gtaagtattttttttctgtattgggttgatgcaaattttttactgtgttc----cacacttgttaatcataaactttcagTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
|| ||||| | | | ||| || ||| ||| || || | | |||| | | ||| ||| || || | | | | ||| || |||| | || ||| || |||| ||||||| |||||||||||||||||||||
tccttatgtgaggattggctagaattatttctcctatctatgtatatgggtttgattatttgaagtttttacagtatatatgttggttttg--tttttagttTTGCTGGGAAGAAGAAATAATGATGT-CTCGGAC--ACAGCTTTACGCATTGTAGCTAGCATGAAGAGAGATTGGATGCAG
upper sequence: AT2G45100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G093422_T01 (Zea mays), 3'ss of exon 1
------------------------gtaagtattttttttctgtattgggttgatgcaaattttttactgtgtt--ccacacttgttaatcataaactttcagTGTTATTGAAA---GGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG--------------
|| ||||| | | | ||| || ||| ||| || || | | |||| | | ||| ||| || || | || | |||||| | || | || ||| || |||| ||||||| |||||||||||||||||||||
aagatccttatgtgaggattggctagaattatttctcctatctatgtatatgggtttgattatttgaagtttttacagtatatgttggttttg--tttttagTTTTGCTGGGATTGGGAAGAAGAAATAATGATGTCTCGGACACAGCTTTACGCATTGTAGCTAGCATGAAGAGAGATTGGATGCAGGCAGGTGTTTCCTC
upper sequence: AT2G45100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G096389_T02 (Zea mays), 3'ss of exon 8
------------------------gtaagtattttttttctgtattgggttgatgcaaattttttactgtgtt--ccacacttgttaatcataaactttcagTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
|| ||||| | | | ||| || ||| ||| || || | | ||| | | ||| ||| || || | | | | ||| || |||| | || ||| || |||| ||||||| |||||||||||||||||||||
aagatccttatgtgaggattggctagaattatttctcctatctatgtatatgggtttgattatttgaagtttttacagtatatgtcggttttg--tttttagTTTTGCTGGGAAGAAGAAATAATGATGT-CTCGGAC--ACAGCTTTACGCATTGTAGCTAGCATGAAGAGAGATTGGATGCAG
upper sequence: AT2G45100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G109651_T01 (Zea mays), 3'ss of exon 7
gtaagtattttttttctgtattgggttgatgcaaattttttactgtgttccacacttgttaatcataaactttca-gTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
| | | || || || | | ||| || ||| || | ||| | | || | | | | | | || | || || || ||| || |||| ||||||| |||||||||||||||||||||
atggggctgattatttgaggttttcacagtatatattcatt-ttgt-ttttaggtttgctgggaagaagagataatgctgtctcagacacagctttttctcgAGAAGTCTCAGACACAGCTTTACGCATTGTAGCTAGCATGAAGAGAGATTGGATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggttgatgcaaattttttactgtgttccacacttgttaatcataaactttcagTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
tgttaat putative branch site (score: 3)
ctttc putative PPT
ttaatcataaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattttttttctgtattgggttgatgcaaattttttactgtgttccacacttgttaatcataaactttcagTGTTATTGAAAGGTGCACACAATAATAAACTCGTGCTAACGGCTACACACATTATAGCTAGTATGAAGAGAGATTGGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA