Sequence
atgc intronic sequence ATGC exonic sequencegtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42990.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
| ||| || | | |||| | || | | | | ||| | | ||| ||| |||| || ||||||||| ||||||| ||||| ||||| |||||||| || ||||||||||| |||||||| ||||||||||||||||| |||| || | ||
-----------------gttacatattttctctacatcaccttgttgaattggtgggtcttgct-------tttgactgcaatacattaccgattgca------gCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
||| || || ||| ||| | | | ||| || | | || | | ||||| |||| | || | | |||||||||||| | || || || || ||||| | ||||||| ||||||||||| || || ||||| || ||||||||||||||||||| ||| |||||||
---gtgacacttagtca-tcatactacttgatctattca--aacctcggtgctctcactccatagccagactctaactagctagaat-----gtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 5
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
| |||| ||| || | | | | | | ||| ||| || | | | || ||||||||||| | ||||||||||| ||||| | |||||| || |||||||| || || ||||| | |||||||||||||||||||| || | |||
----------------------gttacatatttcctctacatatccttgttcaatcggtgggtcttgct-ttctgactgcaatacatacatg-taccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGGTCACCAAAGGAGACCACGTGGTGGTTCCATGACGACACTGTGTGATGGG
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 5
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
| ||| ||| | ||| | | | | || ||| |||| | | ||||| |||| | | || || |||||||| || || || || || ||||| | ||||||| ||||||||||| || || ||||| || ||||||||||||||||||| ||| ||||
---gtagcgtttagtcttactaactactcgat-ctattaaaacctcag-tgccctgactccataatcagactctaactagctaacaatgcatttgttg----cagCAACGTCCAGTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGA
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018447_T02 (Zea mays), 3'ss of exon 5
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT----------
| ||| ||| | ||| | | | | || ||| |||| | | ||||| |||| | | || || |||||||| || || || || || ||||| | ||||||| ||||||||||| || || ||||| || ||||||||||||||||||| ||| ||||
---gtagcgtttagtcttactaactactcgat-ctattaaaacctcag-tgccctgactccataatcagactctaactagctaacaatgcatttgttg----cagcaacgtccagTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGAGCGCCTGTCA
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 5
--gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
||| || | ||| ||| || ||| || || | | | || || || | | | ||| | | || | | ||||||||||| ||||| || || ||||| |||||||||| || || || || || || ||||||||||||||||||||||| ||||| || |||| ||
tggttattatttaagattcttcagg---tgaatttaggtaggtcatcgatccatcatggg--tgtcatttcggcttaataactctttacttt--atttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAT
upper sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattg-tcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
|||| | | || || ||| || ||| | | | | | | | || || ||| | ||| | | ||||||||||| ||||| || || ||||| |||||||||| || || || || || || ||||||||||||||||||||||| ||||| || |||| |
-----attatttaagattctac-tggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
ctcttac putative branch site (score: 3)
ttactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG