Sequence
atgc intronic sequence ATGC exonic sequencegtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G47510.1 |
intron # | 8 |
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 8
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
| | || || | ||| | | | | | | ||| ||| | | | || |||||||| |||||||||||||| ||||| || || || ||||||||||||||
----gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatca--tattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
| ||| | | || |||| | ||| | | || |||| || |||||| |||||||| |||||||||||||| ||||| || || || ||||| ||||||||
---------gtactatactgctaatgtttgttttctt-tacaaattaacacta--ctgataattattttgctgag----------cagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtt---tggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
| ||| | | | || | ||| || ||| |||||||| | || |||||| || ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||||||
----------gtctgcaacttgaagtattaagttttta-actgttctttcccccact-aggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ18116 (Selaginella moellendorffii), 3'ss of exon 6
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaact-tgctggaaatgtttg-gccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
|| || | ||| | | || |||| ||| | ||||||||||||||||||||||| || || || || | ||||||||||||||
------------------------------------------gtaggagcgcgctcttacttctgattgctctctaaattcttgtggcagCTTGCACAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGGMapped 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: TTAAGTATGGACTAAATAGAGTCACCTGCACTCTTCCTCGCCTCTATCAG CTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
genomic: TTAAGTATGGACTAAATAGAGTCACCTGCACTCTTCCTCGCCTCTATCAGgtttgggaaa ... gtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
EST:
gi|164069209|gb|ES171603.1|ES171603EST: ACCTGCACTCTTCCTCGCCTCTATCAG CTTGACACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
genomic: ACCTGCACTCTTCCTCGCCTCTATCAGgtttgggaaa ... gtttggccagCTTG-CACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
gtctaac putative branch site (score: 2)
agtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA