Sequence
atgc intronic sequence ATGC exonic sequence...ttctgcgtcaccagatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30790.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g08350.1 (Oryza sativa), 3'ss of exon 2
ttctgcgtcaccagatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
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--gtaagtcaagtgggaggtagaata--ttcagcaatagttttttttttcatgctcaattgaaattgctgct-tactttcttttacaaattttaatatagATGAACTGTGTGCAACTGGAGAACTGCTTACACGAGGCAAGAGAAGAGGCCCGCACAAACAAATGTTCAGCTGACAGAAGGGCTGTTGAGTATGATGCCC
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G119571_T01 (Zea mays), 3'ss of exon 2
ttctgcgtcaccagatagcttgtgcaccttacacat-tataggaacc------tttccctctaaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
| ||||| | | || | | || || | | || | | ||| | ||| ||| || | | | ||| ||| | | |||||||||||||| ||| | || ||||| |||||||||||||||||||| |||| || | || | |||| | || ||| | ||||| ||| |
--gttagtcacaaaaatctatgataatttcactgatatgtgcaaatcacaataatcaccttcatattcttattcctctgattgccccctctacgcattttgatatagATGAATTGTGCACATCTTGAAAACTGTTTACATGAAGCAAGAGAAGAGGCCCGAACAAACAAATGCTCATCTGACAGAAGGGCTGTTGAGTATGATGCTC
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G143445_T01 (Zea mays), 3'ss of exon 2
-----ttctgcgtcacca-gatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctgatgtggtatacat--tactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
| | | | |||| || | | || | | || || | ||| || | ||||| | | ||| ||| | || |||||||||||||||| | || ||||| |||||||||||||||||||| |||| || | ||| | ||||| | || ||| | ||||| ||| |
gttagtcataaaaatctatgataactccactgctctgtgcaaatcgcaatgatcaccttccatattatttctgtgaatgtgattctccctctacatattttgatgcagATGAATTGTGCGCACCTTGAAAACTGTTTACATGAAGCAAGAGAAGAGGCCCGAACAAACAAATGTTCAGCTGACAGAAGGGCTGTTGAGTATGATGCTC
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G152844_T01 (Zea mays), 3'ss of exon 4
-----ttctgcgtcacca-gatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctg---atgtggtat--acattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
| | | | |||| || | | || | | | || | ||| || |||| ||||| | | ||| ||| | || |||||||||||||||| | || ||||| ||||||||||||| |||||| |||| || | ||| | ||||| | || ||| | ||||| ||| |
gttagtcataaaaatctatgataactccactgctctgtgcaaatcgcaatgatcagcttccatattcttgtttctgtgaatgtgattctgtctctacatattttgatgcagATGAATTGTGCGCACCTTGAAAACTGTTTACATGAAGCAATAGAAGAGGCCCGAACAAACAAATGTTCAGCTGACAGAAGGGCTGTTGAGTATGATGCTC
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G422537_T01 (Zea mays), 3'ss of exon 16
-----ttctgcgtcacca-gatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctg---atgtggtat--acattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
| | | | |||| || | | || | | | || | ||| || |||| ||||| | | ||| ||| | || |||||||||||||||| | || ||||| ||||||||||||| |||||| |||| || | ||| ||||| | || ||| | ||||| ||| |
gttagtcataaaaatctatgataactccactgctctgtgcaaatcgcaatgatcagcttccatattcttgtttctgtgaatgtgattctgtctctacatattttgatgcagATGAATTGTGCGCACCTTGAAAACTGTTTACATGAAGCAATAGAAGAGGCCCGAACAAACAAATGTTTAGCTGACAGAAGGGCTGTTGAGTATGATGCTC
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0037g00730.t01 (Vitis vinifera), 3'ss of exon 3
---ttctgcgtcaccagatagcttgtgcaccttacacattataggaacctttcc-ctctaaatttttacctctga-tgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
||| | || || ||| ||| | ||| ||| | || | ||| ||| | ||||| || || | | | | | | | || | ||||||||||||| || |||||||| || |||||||||||||||| ||||| ||||| || || ||||||||||| || || || || |||||| ||||
cttgtctttggcagcat-tagtttg---attttat-catcacagacatgtttgaattctgacttttttccactttctcttctctctgtggacactctgttaacagATGAATTGTGCTCACTTGGAGAATTGTCTACATGAAGCAAGAGAGGAAGCTCAGACTCACCTCTGTGCTGCTGACCGGAGGGCCTCGGAGTATAGTGCAT
upper sequence: AT4G30790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S71_106V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------ttctgcgtcaccagatagcttgtgcaccttacacattataggaacctttccctc--------taaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
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gttggttggtaaacttgagtttgccactgcagaatgctgggggcttatgtgtggtatggtattttgtcaattctccatctgttctttgaagtttgcatctgctgagggcactttctttagttacggcatggttcaaattctaaattttttta-attggtaatcatgttgcagATGAATTGTGCGCATCTGGAGAACCGGCTGCACGAAGCAAGAGAAGAGGCTCGAACAAACCTTTGTGCAGCTGATCGAAGAGCTGCTGAGTATAGCGCATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125152414|gb|EL184066.1|EL184066EST: AGAGTTGGAAACGAATCAGAAGCTTCTCGAAGAATCCCAG ATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCC
genomic: AGAGTTGGAAACGAATCAGAAGCTTCTCGAAGAATCCCAGgtttggcaga ... ttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttccctctaaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
ctatttt CT-rich tract
tatacattactatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgcgtcaccagatagcttgtgcaccttacacattataggaacctttccctctaaatttttacctctgatgtggtatacattactattttggttgtagATGAATTGTGCGCATTTGGAGAACTGCTTACATGAAGCAAGAGAAGAAGCCCAGACCCATCTTTGTGCTGCTGATCGTAGAGCTTCTCAGTATACTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - caccaga
- - - - - - - - - - - - - -cttacac