Sequence
atgc intronic sequence ATGC exonic sequencegttagacccggtttatctctcaatgataacctattcttctagatgttcatgtttagagctactttccttatttgctttgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G69490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G06150.2 (Glycine max), 3'ss of exon 1
--gt-tagacccggtttatctctcaatgataacctattcttctagatgtt-catgtttagagctactttccttatttgctttgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
|| | | || ||| | | ||| || | | | ||||| ||||| | | || | | ||| | | | | |||||| |||||||| ||||||||||| |||||||| ||||| ||||| |||| || || |||||||| || || || || || | ||| | || || || ||
ctgtgtgaatattgtctatatttgaat-atgttgaaccttataatatgtttcatgtgcatgtttcacttgttcttacatgttgattgctcatgaaatacagATAAAACAGACTTTGGAGAAAAGGAGTGGTACTTCTTTAGCCCACGAGAGAGGAAGTATCCAAATGGGGTGAGGCCTAATAGAGCAACCGTGTCTGGGTA
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G04400.1 (Glycine max), 3'ss of exon 1
gttagacccggtttatctctcaatgataacctattct-----tctagatgttcatgtt-tagagctactttccttatttgctt--tgttcgttttgtatt---tacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
| | | | | | | || | || | || || | ||| | | ||| | || | ||| | || || || | |||| |||||||| |||||||||||||| ||||||||||| | || ||||| || || || ||||| || || || || ||||| ||| | || || || ||
--------cagctgaaattgtagttgcaaattgttttaaaaaccttgacatgaatggtattatattacatctctaacacacttgttattaaattaccatggaatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTACTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACCGTGTCAGGGTA
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G35630.1 (Glycine max), 3'ss of exon 1
------gttagacccggtttatctctcaatgataacctattcttctagatgttcatgtttagagctactttccttatttgctttgttcgttttgtatt-tacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
|| | || | || | | | ||| | | ||| | ||| | | | | | ||| | | | | | | |||| |||||||| |||||||||||||| ||||||||||| || || ||||| || || || ||||| || || || || ||||| ||| |||| || || ||
accgaaattgcaatcg--cggaccctttttaaaatcct--taacatgaatggtattgtattacatctcctaacacacttgttattaacttaccatggaatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTAGTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACTGTGTCTGGGTA
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G12220.4 (Glycine max), 3'ss of exon 1
gttagacc-cggtttatctctcaatg-ataacctattcttctag-atgttcatgtttagagctactttccttatttgctttgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
| ||| || ||| | | ||| | | || || || |||||||||| | | || | | ||| | | | |||||| |||||||| ||||||||||| |||||||| ||||| || || |||| || || |||||||| || || || || || | ||| | || || || ||
ttgtgactattgtctatatttgaatatgttgcaccttattataatatgttcatgtgcatgtttcacttgttcttacatgttgatttctcatgaaatacagAAAAAACAGACTTTGGAGAAAAGGAGTGGTACTTCTTTAGTCCACGAGAGAGGAAGTATCCAAATGGGGTGAGGCCTAATAGAGCAACCGTGTCTGGGTA
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0026g02710.t01 (Vitis vinifera), 3'ss of exon 1
gttagacccggtttatctctcaatgataacctattcttctagatgttcatgttta---gagctactttccttatttgctttgttcgttttgtatt-tacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
|| || | || || | | || || ||| || ||| ||||| | | | || ||| ||| | | | || | | ||||||| | || |||||||||||||||||||||||||| ||||| | || | || ||||| || || | ||||| ||||| || | || ||||| ||
gtgagtttcatttcattggt--aggagtacatat-ctcaactatgctcatgctcatgtaactcgtgtttaacctttaatttttactatatgggctgtgcagAGAAGGCGGAATTTGGAGAAAATGAGTGGTATTTCTTTAGCCCGCGTGACCGTAAGTATCCCAATGGGGCTAGACCCAACCGAGCTACAGTGTCCGGCTA
upper sequence: AT1G69490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 1
----gttagacccggtttatctctcaatgataacctattcttctagatgttcatgtttagagctactttccttatttgctt-tgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
|| | || | | | | | || ||||| ||| ||||| | | | || | | | | | | ||| ||| || || ||||| | || ||||||||||||||||| |||| ||||| || ||||| |||| |||||| ||||| ||||||| || || ||
taagcttctcgcaaattgaacggaagttagttatttaaacttct--gtgtccatgtgatcattaaacaccgaggttggagtataattaaaactttgctgcagGAAAAGCAATATTCGGAGAGAGAGAATGGTATTTCTTCAGCCCACGAGACAGAAAGTACCCAAATGGAGCCAGACCCAACCGAGCAGCTGCCTCTGGGTAMapped 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|47830767|gb|CK120451.1|CK120451EST: CATCATCCCAGAAGTTGATATCTACAAATTCGACCCATGGCAATTACCCG AGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAA
genomic: CATCATCCCAGAAGTTGATATCTACAAATTCGACCCATGGCAATTACCCGgttagacccg ... gtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAA
EST:
gi|116411169|gb|EG453761.1|EG453761EST: CATCATCCCAGAAGTTGATATCTACAAATTCGACCCATGGCAATTACCCG AGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAA
genomic: CATCATCCCAGAAGTTGATATCTACAAATTCGACCCATGGCAATTACCCGgttagacccg ... gtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttcatgtttagagctactttccttatttgctttgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
ttttgtattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagacccggtttatctctcaatgataacctattcttctagatgttcatgtttagagctactttccttatttgctttgttcgttttgtatttacagAGAAAACAGAGTTTGGAGAAAATGAGTGGTATTTCTTCAGCCCTAGAGAAAGAAAATATCCAAACGGAGTCAGACCAAACCGGGCAGCTGTTTCCGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT