Sequence
atgc intronic sequence ATGC exonic sequenceATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51590.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G130889_T03 (Zea mays), 5'ss of exon 9
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgtt--aacgtttgcttcttcattttcag
|| || ||||| || ||||| ||||| ||||| ||| | ||||| || ||||||||||||||||| ||| |||||||||||||||| || ||| |||||| | ||| | |||| | | | | | |||| ||| | || || | ||| || ||| ||||| | |
CTTGACGGGGAATAAAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGCATAGAATCTGGATATGTGGGACTGAGAGATgtaggattcc--tca---tgacttctattgttga---atttctgctgagtaa-------catttgtctgacaactgttcttggaacatttgcctttag--------
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G128914_T01 (Zea mays), 5'ss of exon 13
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcag
|| || ||||| | ||||| ||||| ||||| ||| | ||||| || ||||||||||||||||| || ||||||||||||||||| || ||| |||||| ||||| | | || | || | ||| || || | ||| ||| | || | | ||| |||| ||||||
CTTGACGGGGAATACAACATACCAAGATTGGGGGTGGGACATATTCCAGGCATTTGAGAAGAACTCCCGTGTAGAATCTGGATATGTGGGACTGAGAGATgtaggtttcct-catgactcccattgatgaatt--------tctgcggaataacattt--gtctgacacaactattgttggaacatttg--tcttcag------
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G23730.1 (Glycine max), 5'ss of exon 13
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaac-gtttgcttcttcattttcag
||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||| |||| || || ||||| || ||||||||||||| | | | || | | ||| | | | | | | | | | | | ||| | | || ||| | || || || |
TCTAACTGGCAACAAAACATACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGCATAGAGTCAGGCTATGTTGGACTGAAGGATgtaagca-cacctcaatttcacatctaataatgtgtttttgtttgc-attattattgtttttgtatgaagtacatcctatcaaaagttagtttatttgttct---
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G02290.1 (Glycine max), 5'ss of exon 12
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgtt---aacgtttgcttcttcattttcag
||||||| ||||| || || ||||| ||||| ||||||||||||||||| |||||||||||||| || |||| || || ||||| || ||||||||||||| | | || | | | | ||| | | | | | || ||| | || || | | || ||| | | || || |
TCTAACTGGCAACAAAACGTACCAAGAATGGGGTTGGAATATATTTCAAGCTTTTGAGAAGAACTCCCGGATAGAGTCAGGCTATGTTGGACTGAAGGATgtaag---caaacctcaatt-tcacatctaataatgtgtttttgtttacattattattgtttctgtgtaaagtacatcctatcaaaagttagatcatttgttct---
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G06600.1 (Glycine max), 5'ss of exon 13
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgt-ttgcttcttcattttcag-
|| ||||| ||||| ||||| ||||| ||||| |||||||| |||||||||||||| || || ||||| | || | |||||||| || | || |||||||| | | | | || |||| | ||| | || | || || | || | ||||| | | || | ||| |||
TTTCACTGGAAACAAAACATACCAAGAATGGGGTTGGAATATTTTTCAAGCATTTGAAAACAATTCTCGGATTGAGACAGGATATGTTGGACTCAAAGATgtaaga---aattca---taaactgcttcaatattttctcctacatgatttactctcattctcaaccctgaaaaagttgtgcatgcatttgtgaagtattctcata
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 5'ss of exon 8
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcc--tttccatctttcggaaacacgttgttaacgtttgcttcttcattttcag-----
|||||||| | ||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||| ||| |||| || |||||||| || |||||||||||||| | | | || | | || || | || ||| ||| ||| ||| | | || || | ||| || | || | | | ||
TTTAACTGGCAGCAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATATGTTGGACTGAAGGATgtaagt----------acactcttcaaactcactaatccctacttcagactggctgatttgcatttttagtatttacttt-tgaactttgattcctgaaatcttagaacat
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 5'ss of exon 13
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcat-tttcag-----
|||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||| ||| |||| || ||||| || || |||||||||||||| | | | || | | || || | || | | | | ||| | | || | |||| ||| | | | | ||
TTTAACTGGCAACAAGACATACCAAGAGTGGGGTTGGAACATATTTCAAGCATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagt----------acactcttcaaactcactaatccctacttcagactgactgattcgcatttttagcatttacttttgaactttgattcctgaaatcttagaaaatMapped 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|116428419|gb|EG471011.1|EG471011EST: CATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGAT GTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAG
genomic: CATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcg ... tcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTAACTGGGAACAAGACATATCAAGAGTGGGGATGGAATATATTTCAAGCATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG