Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattacttcaaacatgtttgtaattgctaggttacatgctttgtcgccaatctaatattaccttggttattctatgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54960.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 7
---------gtaagcattacttcaaacatgtttgtaattgctaggttacatgc---tttgtcgccaatcta-atattaccttggttat---tctatgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
| | ||| | || | | | | | | | |||| | ||||| | | | | | | | ||| || ||| ||||| || || |||||||| ||||||||||| |||||||||| ||||| ||| | || ||||||||||| || | |||
aagtaaaacattattgttattcttaaaagctatttcagtatcatgttatttttctatttgttcttactttttagctgatccgtactatccatcctctcagCTCTGCAGACATCTGGAGTGTGGGATGCACAGTTATTGAAATGGCTACTGGTAAACCACCATGGAGCCAGCAGTACCAGGAG
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 7
--------gtaagcattacttcaaacatg-tttgtaattgctaggttacatgctttgtcgccaatctaatat---taccttggttattctat----gcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
|| | | | | ||| | || ||| | | | ||| | ||| | | || | ||||| | ||||||||| ||||| ||||||||||| |||||||| |||||||||| ||||| ||| | || ||||||||||| ||| ||||
aatgtactgtgatctgaaatagaaaactacttcagaatcgtgttgccttttttttttggtctaatttggcacacccgcccttactattccgttctctcagTTCTGCAGATATATGGAGTGTAGGGTGCACAGTCATTGAAATGGCCACTGGCAAACCACCATGGAGCCAGCAGTATCAAGAA
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G064613_T03 (Zea mays), 3'ss of exon 7
-----------gtaagcattacttcaaacatgtttgtaattgctaggtta--catgctttgtcgccaatctaatattaccttggttattct---atgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
| ||| | || | ||| | | | || || ||| ||| | | | | | |||| | ||||||||||||||||| |||||||| || ||||| || |||||||||| | || ||| | || |||||||| ||||| |||||
aattcagaacaacttacgatacattctgtatttctgttgctcccaactttgttatcttttaaattaaatttgaattaatacttattatccattggtgcagTTCTGCTGATATCTGGAGTGTTGGTTGCACGGTAATTGAAATGGCAATAGGCAAACCCCCATGGAGCCACGAATATCAAGAG
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 7
-------gtaagcat-tacttcaaacatgtt-tgtaattgcta-----ggttacatgctttgtc---gccaatctaatattaccttggttattctatgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
|| || | | | || ||||| || |||| || | | ||| | | | | ||| || | || | ||| || || |||||||| |||||||| ||||| || || ||||| |||| |||||||| ||||||||||||| | || |||||
aatctcattatgcttctgcatctgtgatgttctgacattgataatgaagatcacaaattcttgctatattattctgattattttcaaaataatttat-tagCTCGGCTGATATATGGAGTGTTGGATGTACCGTTATTGAGATGGCCACTGGAAAGCCTCCTTGGAGCCAAAAGTACCAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctaggttacatgctttgtcgccaatctaatattaccttggttattctatgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
atctaat putative branch site (score: 3)
ttattct putative PPT
aatctaatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattacttcaaacatgtttgtaattgctaggttacatgctttgtcgccaatctaatattaccttggttattctatgcagTTCTGCTGATATTTGGAGTGTAGGATGCACAGTGATTGAAATGGTGACTGGAAAAGCTCCTTGGAGCCAGCAATATAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG