Sequence
atgc intronic sequence ATGC exonic sequenceTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtcttcaaagattcatcatcttgtttttatttcctcttttttttcatctgatttgtctcaattgatggatactgcaag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45800.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45800.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA18G46460.1 (Glycine max), 5'ss of exon 2
-----------------------------TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATG---ATCATCTGg--taatgtcttcaaagattcatcatcttgtt---------tttatttcctcttttt--tttcatctgatttgtctcaattg--atggatactgcaag------------------
|| || || ||||||||||| |||||||||||||| ||||||||||||| ||||||||| ||||| |||| |||| | || || |||| | | || | | || | | | |||| || || || | | | | | |||| ||| ||| || | || ||| | || |
ATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAGgtaagatgtaaccatcctttgttcatcactttgtttactatttttattcaaccgcaatctcattgagtacaaattcatatgcacctgtcactttctattgacttggctaacatgttatgttgttttcatgaccataattgcggcacag
upper sequence: AT2G45800.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA09G39740.1 (Glycine max), 5'ss of exon 2
-----------------------------TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCA----TCTGgtaa-tgtcttcaaagattcatcatcttgttt-----------ttatttcctcttttttttcatctgatttgtctcaattgatggata---ctgcaag------------------
|| || || ||||||||||| ||||| |||||||| ||||||||||||| ||||||||| ||||| |||| |||| | | || ||| | || | | | | || | | || |||| || |||| | | |||| ||| ||| || | || | | | || |
ATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAGgtaagatgtaaccatcttttgttcagcactttgtttactatttttattcaaccacaatctcattaggtacaaattattatgcacctgtcactttctattgacttggctaacatgttatgttgtttttcatgaacaaaattgcggcacag
upper sequence: AT2G45800.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA07G08020.1 (Glycine max), 5'ss of exon 2
-----------------------------TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtcttcaaagattcatcatcttgtttttatttcctc------ttttttttcatctgatttgtctcaattgatggatactgcaag----------------
|||||| || ||| |||| || |||||||||||||| ||||||||||||| ||||||||| || |||||| | ||| | | || ||| ||| | || || | || | | | | | | || | | | || | ||| | || ||
ATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCGgtaagacgaagacc-atcttttggccaatctttttgtgctgttctcata-atccaacctcaaagtacaagtaggtaggaaaatgtcactttctgttacttatgctaatgaaactatgttgttttcttgtaaatgttgcag
upper sequence: AT2G45800.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G01590.1 (Glycine max), 5'ss of exon 2
-----------------------------TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtcttcaaagattc---atcatcttgtttttatttcctctt-------------ttttttcatctgatttgtctcaattgatggatactgcaag----------------
|||||| || ||| |||| || |||||||||||||| |||||||| |||| ||||||||| ||| |||||| | ||| | | || ||| ||| | | || ||| | | | | | | || | | |||| | ||| | || ||
ATGAGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGAAATTTCAGCAAGAACTTTGgtaagacgaagacc-atcttttggcccatctttttgtgctgttctcatatttctcatataatccaacctcaaagtacaagtaggtaggaaaatgtcactttctgttatttatgctaatgaaactatgttgttttcttgtaaatgttgcag
upper sequence: AT2G45800.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 5'ss of exon 2
-----------------------------TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtcttcaaagattcatcatcttgtttttatttcctcttttttttcatctgatttgtctcaattgatggatactgcaag
|| ||||| || || || || || ||||| ||||| || |||||||||| ||||||||||||||| || | |||| || | || ||| | ||| | ||| | |||| | | | || | || ||| | |
ATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACATgtgagacttttttttaaaaaatttatttggca-----ttctgggtttctttttcttaatgagctaactcctatggttctgcatgaatag-----------------------Mapped 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|19878067|gb|AU238898.1|AU238898EST: ACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTG ACTCGAACTCCAAGCAAGTTATCATCATTCTTCAGTGGAACACAAGACAAA
genomic: ACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtctt ... atactgcaagACTCGAACTCCAAGCAAGTTATCATCATTCTTCAGTGGAACACAAGACAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAGGAAAGACCGAGAAGCCCAATGATCATCTGgtaatgtcttcaaagattcatcatcttgtttttatttcctcttttttttcatctgatttgtctcaattgatggatactgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC