Sequence
atgc intronic sequence ATGC exonic sequencegtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G47510.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
| || || ||| || | || | | | ||| | || | | ||| || | || | | ||| | | | | | ||| ||||||| || |||||||||||||| ||||| ||||||||| | || ||||| || ||||| ||||||||||||||| ||
-------ttggtt-taggattactttga-aacagagtgttaattccatgctt--tacctaaggcgttcctttcat-----ttatttaaatacctaaatccaatctgtctttttcagATTTGATGCCAAAATAGCTGCTGCAGTGGCTGAGGAAACAAACCTACCCTTTGTGACAGCAGAGAACAAGTTTGAAGCTTTG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 8
gtatatctcatttctaatt--ttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
| ||| || | | | | ||| | | | | | | || |||| || |||| | || | | || || ||| | || | ||||||||||| |||||||| || ||||||||||| |||||||| |||| |||||||| |||||||| |||||||| || ||
-------ttattatgaaataataaataccaaacctaccttttaagg----ctgaagaaaatatgtggtttaactaaaga------taaacagtgataattttctagatgaa-attcagGTTTGATGCCAAGATAGCAGCAGCAGTAGCTGAGGAAACAAATCTGCCTTTTGTCACGGCAGAAAATAAGTTTGAGGCCTTG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
| | | | ||| | | | || || |||| | || | | | | || || | | | ||| | || | ||||||||||| |||||||| || ||||||||||| |||||||| |||| ||||| || |||||||| |||||||| || ||
--acaagcttgtagtggtttattatgctgaagaaaatatgtggtttaacttctaaagaaataaatttggataaacaatgataatttcctggatgaa--------------attcagGTTTGATGCCAAGATAGCAGCAGCAGTAGCTGAGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
|| | || ||||||||| | | || ||| | || | | | | | || || | | | ||| | ||| | | ||||||||||| || ||||| || ||||||||||| ||||| || |||| ||||| || |||||||| |||||||| || ||
ttactacaagcttgtaattttatgctgaagaaaatatgtt--gtttaacttttaaagaaataaatttggataaacaatgataatttcctgga-taaaatt-------------cagGTTTGATGCCAAAATAGCAGCAGCAGTAGCTGAGGAAACCAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 9
-gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
|||| | | ||||||| | || || | || | || ||| | ||| | ||| | |||||| || || || |||| | | | | | | | ||||||||||||||||||||| ||||| || || |||||||| || ||||| ||||| |||||||||||||||||||| |||
agtatgt---gcatttaattttctctcaatcttattat--gaagtccatttatcc-atattagttgtttt----------ttagttcatgatagtca-atttttgagcttcatttagGTTTGATGTAAAGATAGCTAGAGCAGTTGCCGAGGAAACAAATTTACCATTCGTCACAGCAGAAAACAAGTTTGAAGCACTGMapped 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|116480251|gb|EG522843.1|EG522843EST: CTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG GTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST:
gi|164069209|gb|ES171603.1|ES171603EST: TTGACACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG GTTTGATGTAAAGATAGCTGC
genomic: TTG-CACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGC
EST:
gi|125013157|gb|EL085426.1|EL085426EST: GGACAGGATTAAACACTAAGAAAGG GTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: GGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
tagtaac putative branch site (score: 1)
tttattagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC