Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaatgtttaacaaaatttcttgaagttgcatcatttctattgtgccctatttgtttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12000.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 7
gtaa-gtaaatgtttaa--caaaatttcttgaagt-tgcatcatttctattg--tgccctatttgtt--tacatgctgtatca--cattt-tcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
| | | || || || || | | | ||||| | | || || | | | ||||| || | | || || || || |||||||||| || |||||||||||||||||||| ||||||||||| || || ||||| ||||| ||||| || | | ||||| ||||||
gcagtgctaacgtgtagtccatgaatattggaagtatataacagaattacagatcggacattttgtcaataaaaattctaacaagcacttgctcttgcagTTGTGAGGCTTATGGGTCGTGCTGCTTCTCACATTACGCTGGAATGCGCTTTGCAAACACACCCCAATGCTGCACTCATTGGGGAAGAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 7
--gtaagtaaatgtttaacaaaatttcttgaagttgcat-catttctattgt-gccctatttgtttacatgctgtatcacat-------tttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
|| || || | || | | || | ||| | || ||| | || || || | || || | || |||| | | ||||||||| | |||||||| || || ||||| ||||||||||| || ||||||||||||||||| |||||||| || |||||||||||||||
atatatatatatatatatccgtctatcgtatgattgtgtgtgctttcattattgctctgttggatttcaaacaataagacatgagatcatctgtctgcagTTGTGCGGCTTATGGGGCGGGCGGCTTCACACATTACGCTGGAATGTGCTTTACAAACTCATCCAAACATTACTATTATTGGAGAAGAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 7
-----gtaagtaaatgtttaacaaaatttcttgaagttgcatcatttctattgtgccctatttgtttacatgctgtatcacat-------tttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
| ||| || || | ||| || | |||| | ||| | ||| | || || | || |||| | | ||||||||| | |||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||| || |||||||||||||||
gacatttggaatcatgcttt-caccagcctatgattgtgtgtgctttcattattgctccattggatttcaaacaataagacatgagatcatctgtctgcagTTGTGCGGCTTATGGGGCGTGCAGCTTCACACATTACGCTGGAATGTGCCTTACAAACTCATCCAAACATTACTATTATTGGAGAAGAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 7
--------------gtaagtaaatgtttaacaaaatttcttgaagttgcatcat--ttctattgtgccctatttgtttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
|| || ||| | || | || | ||| | |||| || | | | | ||| | || ||||||||| | |||||||| ||||| ||||| |||||||| || || |||||||| |||||||| |||||||| || |||||||||||||||
ctctctctctctccgtgtgtgtgtgtgtgtttgtgttacctg----ttcattgttattctgctgagttttgaacaatgg-gtaagatatggccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCGCACATTACACTGGAATGTGCTTTGCAAACTCATCCAAACATTACTATTATTGGAGAAGAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 5
-------gtaagtaaatgtttaacaaaatttcttgaagttgcatcatttctattgtgccctatttg----tttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
| | | | | || ||||| |||| | | ||| | | || | || ||||||||| | |||||||| ||||| ||||| |||||||| || || |||||||| |||||||| || ||||| || |||||||||||||||
tctctctctctctctcccctgggtgtgtgtgcgtgttacctgttcattgttattctactgagtttcgaacaatgggtaagatacagccacttgtctgcagTTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAG
upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 7
-------gtaagtaaatgttt-aacaaaatttcttgaagttgcatcatttctattgtgccctatttgtttacatgctgtat-cacattttcattg--cagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
| ||| | || | || | ||| | ||||| || | ||| | || || | | | | ||| | |||||||| |||||||||| ||||| || || |||||||| | ||||||||||| |||||||| |||||||| || |||||||| ||||||
gatttcaactcttttatgctccaatttacatttccttatttgttttatttcctttcttttatatgattgtaagtggtatttgtatgtttgtgtgcatcagTTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGMapped 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|124888447|gb|EH967349.1|EH967349EST: GATCGGAAACGTCATGATTGATGCAAGGTCGACTGGAAAGTACTATCATT TTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACG
genomic: GATCGGAAACGTCATGATTGATGCAAGGTCGACTGGAAAGTACTATCATTgtaagtaaat ... ttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACG
EST:
gi|116438054|gb|EG480646.1|EG480646EST: GATCGGAAACGTCATGATTGATGCAAGGTCGACTGGAAAGTACTATCATT TTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTT
genomic: GATCGGAAACGTCATGATTGATGCAAGGTCGACTGGAAAGTACTATCATTgtaagtaaat ... ttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcatttctattgtgccctatttgtttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
ttttcatt CT-rich tract
tatttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaatgtttaacaaaatttcttgaagttgcatcatttctattgtgccctatttgtttacatgctgtatcacattttcattgcagTTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA