Sequence
atgc intronic sequence ATGC exonic sequencegtgctggtgtgctaaattttgtattcatctttttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G42920.2 (Glycine max), 3'ss of exon 2
-----------------------------------------gtgctgg---tgtgctaaattt--tgtattcat-ctttttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
|| | | | | | |||| | |||||| | ||| | |||| | | || || | | |||| | | | ||||| ||||| || ||| ||| | | ||| | ||| |||||||||||||| ||||||||||| ||||||| ||||||||||||||||||||
gtactcttatctatttcccttctcaattgctattcattgtggttttagatatttaatcaattcgcttgattcattccccttatcaatacttgtttgtgctgcattcatgttatgaagggttttctcctttcagGACATTACGCAGTCTATCAGTGGCAACGTGAAAGTGACGGGGCAGTGGTTTTATCGTCCCGAAGAAGCCGAGAAAAAAGGTGGTGGAAACTGGCAATCGT
upper sequence: AT4G11560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G02560.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------gtgctggtgtgctaaattttgtattcatctttttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
| | || | || || || | | | ||||| | | || || | | |||| | | | ||||| ||||| || ||| |||| | | ||| | ||| ||||||||||| || || |||||||| ||||||| ||||||||||||||||||||
gtacctcttatctatttcccttctcaattgctattcattgtgattttagatatttaatcaattcgattggttcatgcccgatagataaataaataaatagttgtttgtgctgcattcatgttatgaagggttttctgctttcagGACATTACACAGTCTATCAATGGCAACGTGAAAGTGACGGGGCAGTGGTTTTACCGACCAGAAGAAGCTGAGAAAAAAGGTGGTGGAAACTGGCAATCGT
upper sequence: AT4G11560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G01770.1 (Glycine max), 3'ss of exon 2
-------------gtgctggtgtgc-taaattttgtattcatctttttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
|||||| | | | | |||||| || | | | | | || | || | || || ||| ||||| ||||| ||| | | |||| ||||||||| | ||||||||||||||||| ||||||||||| || | || |||||||| | ||||||||||
tgtgtgggtgagggtgctgttattcattaattttctacaaaatctagatatatcgacctttctctctccaccttcatttggggggttgttttgttgccagGACATTACGCAATCCCTAAATGGCAGCATGATGGTCACAGGACAGTGGTTTTATCGTCCCGAAGAAGCTGAAAGAAAAGGTGGTGGCAGCTGGCAATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
tgcttcttt CT-rich tract
tttgaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctggtgtgctaaattttgtattcatctttttagtttttgttgtgtcgtccgctttgaaataatgacacatgcttctttgacagGATATTACCCAAACTAAAGATGGAAGCATGATGATTCTGGGACAGTGGTTTTATCGCCCCGAAGAAGCAGAGAAAAGGGGTGGTGGAAACTGGCAATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA