Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcattatacacttatctccctctttaacttctcattgcatttgtgattaacagtctctgttcgatttccgtgcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G08790.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G145578_T01 (Zea mays), 3'ss of exon 6
---gtatgtcattatacacttat-ctccctctttaacttctcat-tgcatttgtgattaacagtctctgttcgat-ttccgtgcttggt-ttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
||| || | | | || || | | | ||| ||| ||| || | | ||| | ||| | | || ||||| || |||||||||||||| |||||||| ||||| |||||||||||||| ||||| | | || ||||| || ||||| || || | | | | |
tatatataaaataaaaagttaatgctgtaccaattatgcaacatctgcttttctgttgtgattttaaaacatgatgcacagtgttcgaaaccatttgcagGTTATTGCTGCTGCTCAAGCTGGAAAGCACAATGAAAAAAGAGAAAGTTACGGTGATTCTATAATTATTGACCCATGGGGGACAGTGATAGCTCGACTTC
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G43950.1 (Glycine max), 3'ss of exon 6
gtatgtcattatacactt--atctccctctttaacttctcattgcatttgtgattaacagtctctgttcgatttccg-----tgcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
| ||| | || || | | || || | | | | | | | | | | |||| | || | | || ||||||||| |||||||| ||||| || || |||||||| ||||||||||| || ||||||||| | || || ||||| ||||| || | || || | ||||
ttttgttttaatgtgtttgaaattattagaacaagttactaagataactatcctaggaaatgtgtttcaagtttcaacaagttactaagataattatcagGTCATTGCTGCTGCGCAAGCTGGCAAACATAATGATAAAAGAGAAAGCTACGGTGACACATTAATTATCGATCCATGGGGGACAATTGTAGGTCGATTAC
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 8
-------gtatgtcattatacacttatctccctctttaacttctcattgcatttgtgattaacagtctctgttcgatttccgtgcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
| ||| | || | || | | | || || | | | | |||| | | || | | || ||||||||| |||||||| ||||| || || ||||| || ||||||||||| ||||| ||||| | || || ||||| ||||| || | || ||| | ||||
ttttgttttttgttttaatgtatttgaaatgattagaacaagttacttagataactatctgaggaaatgtgtttcaaaaagttactaagataattatcagGTCATTGCTGCTGCGCAAGCTGGCAAACATAACGATAAAAGAGAAAGCTATGGCAACACATTAATTATCGATCCATGGGGGACAATTGTAGGACGATTAC
upper sequence: AT4G08790.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 6
------gtatgtcattatacacttatctccctc-tttaacttctcattgcatttgtgattaacagtctctgttcgatttccgt-gcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
||| | || || ||| || | | | || |||| | | | ||| || | || | | | | |||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||| ||| | | || |||||||| |||||||| || |||| | |||
tcttggctattttctttaggctttgactcattcatcttgtgtgctatcatgtttgctgctg-cttcatttgtgggaatgatgttgatgaatctgctatcagGTCATAGCTGCTGCACAAGCTGGAAAGCATAATGATAAAAGAGAAAGTTATGGAGACTCCTTAATAATTGATCCATGGGGAACAATAATTGGCCGTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcatttgtgattaacagtctctgttcgatttccgtgcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
gattaac putative branch site (score: 2)
tgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcattatacacttatctccctctttaacttctcattgcatttgtgattaacagtctctgttcgatttccgtgcttggtttatcgtcagGTCATAGCTGCTGCTCAAGCAGGAAAGCATAATGAGAAAAGAGAAAGTTATGGTGACACACTGATCATTGATCCGTGGGGAACTGTAGTTGGAAGGTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG