Sequence
atgc intronic sequence ATGC exonic sequencegtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07290.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
-gtataagctttgtacctttttatgatcaatttg-tgtagatgatgtatcattgttct-ttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
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ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgta-cattatccaatttgaaataaatcaatattgtgccc--tcatcccttt------tttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
----------------------------------------gtataa-gctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaa--------ggaaaaaagcgtttggttacaag-----tttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
| ||| | | | || | || |||| || | | | | |||| |||| |||| | | | | ||| | || || | | || ||| | || || ||||| || ||||| ||||| ||||| |||||||||||||| ||||| |||| | | || || |||||| ||||||| ||||| |||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaat-ttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
gtataagctt-----tgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
|||| | | |||||| || | | | | | || | | || || |||| | | | ||| || || | | | || ||| |||||||||| ||||||||||| |||||||| || ||||| |||||||| ||||| || | | || ||||| | ||| | ||||| |||||||
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaaga--ttaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------gtataagctttgtacctttttatgatcaatttgt-gtagatgatgtatcatt-gttctttagaaaaaaaggaa-aaaagcgtttggttacaa-gtttaaaac-cttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
||| ||| |||| | | | || | || | | |||| | ||| | | | ||| | | | | | | || || | | | || |||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| |||||||||| ||| ||||| || ||| | ||||||||||| |||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
gtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
|| || | | ||| | | | || | |||| ||| | ||||| || ||||| ||||| |||||||||||||||||||| || || || || || | ||| || || || || || || | || |||||||
-------------------------------------------------------gtttgacaccgttgttttcttcgtgcgcattctcattctcgatctta-cagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
| || | |||| | | || | | || | | | ||| | | | || |||| | |||| | ||||| || ||||||||||| ||||| ||||||||||||||||||||||| || || | ||||| || || || | || || || || || ||||
-----------------------gttc--tctgtgaaaaagagagaggag-attttcctacgacttggttctaaaacttgtcattctttgttt-------tcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCCMapped 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|116455509|gb|EG498101.1|EG498101EST: ATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAG GCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCG
genomic: ATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAGgtataagctt ... accttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCG
EST:
gi|125041850|gb|EL114119.1|EL114119EST: ATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAG GCATTCAACGGTAAGAAATGGGAAAAGTTCAACAAGCGAGAAGGTGGCA
genomic: ATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAGgtataagctt ... accttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACA-GCGAGAAGGTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
aaaaaaaggaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataagctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC