Sequence
atgc intronic sequence ATGC exonic sequenceGTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgttgtttgtgatatttgaacaacatgagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48540.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G124091_T03 (Zea mays), 5'ss of exon 1
------------------------GTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgt-tgtttgtgatatttgaacaacatgagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt----
|| | || ||||| || || ||||||||||| || |||||||| || || || || |||||||||||| |||||||||| | ||| ||| | || | | | | | ||| ||| | |||| || | || | | | || | | ||
GATTCGTGGCGCTTGTTTGTGCAGATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatat-----gcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G124091_T04 (Zea mays), 5'ss of exon 2
-----------------------GTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgt-tgtttgtgatatttgaacaacatgagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt----
|| | || ||||| || || ||||||||||| || |||||||| || || || || |||||||||||| |||||||||| | ||| ||| | || | | | | | ||| ||| | |||| || | || | | | || | | ||
ATTCGTGGCGCTTGTTTGTGCAGATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatat-----gcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G124091_T05 (Zea mays), 5'ss of exon 2
GTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgt-tgtttgtgatatttgaacaacatgagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt----
|| | || ||||| || || ||||||||||| || |||||||| || || || || |||||||||||| |||||||||| | ||| ||| | || | | | | | ||| ||| | |||| || | || | | | || | | ||
ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatat-----gcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 5'ss of exon 2
GTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgttgtttgtgatatttgaacaacat--gagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt
|||||| || |||||||||||||||||||| ||||| || ||||| || ||| |||| |||||||||||||||||||| | |||| | || |||| ||| | || | || || | || | || | | ||| | || | | |
GTACTTGTCTTGGGATGATTATTTCATGGCAATTGCGTTTCTTTCAGCTGAAAGATCTAAGGATCCTAACAGGCAGgtcataattgtgtgcccttatgcttgatttgcatttaaaaatttgagcaaaaat-cgaataaaattttctttccaaa-acaatgaaagtaattcccaaatgcMapped 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|125126321|gb|EL171566.1|EL171566EST: TGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAG GTTGGCGCATGTTTGG
genomic: TGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttg ... ggctgtgcagGTTGGCGCATGTTTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACTTATCATGGGATGATTATTTCATGGCGATTGCATTCCTTTCTGCAGAACGATCCAAGGATCCTAACAGGCAGgtaaattttgttgtttgtgatatttgaacaacatgagtatccaaacagttatatatgtgtaagctgctcaaaatgtattatgttcatgatactatatagt
- - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaca