Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25490.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
------------gtttgttgcatctctcttgtgtgctttagatactacttttattgctt--ccttatttagttggtgactgaattatcttt-tacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
| | ||| || || || || | ||| ||| | || | || | ||||| | | || | |||||||||||||||||| | || || ||||| |||||||||| || ||||||||||| |||||| |||||||||| || || ||||||||||| |||||
agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
---------------------------------------------------------------------------------------------gtttgttgcatctctct---tgtgtgctttagatactacttttattgcttccttatttagttggtga---ctgaattatctttta---cggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
|| || | || | | | | || | || | | || | | | ||| || ||| |||| || | |||| ||||||||||||||||| | ||||||||||| || |||| || |||||||||||||| |||||| |||||||||||||||| ||||||||||| |||||
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
----------------------------------------------------------------------------------gtttgttgcatctctcttgtgtgctttagatactacttttattgcttcctt-------atttagttggtgactgaattatctttta---cggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
|| || || | | | || || | | | | | ||| || |||| | |||||| | |||| ||||||||||| ||||| | |||| ||| | || |||| ||||||||||||||||| |||||| |||||||||||||||| ||||||||||| |||||
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 8
----------gtttgttgcatctctcttgtgtgctttaga-tactacttttattgc--------ttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
| | ||| | ||| | | | ||| || | | || | | | | | || ||| | | || || ||||||||||||||| || | |||||||||| |||||||| |||||||| || |||||||||||| |||| ||||| || ||||||||||||||||| |||
agagcttatgatcttatgccaccttctatagagatgcagagtaaaaatcacataacgaaaaaaacttttcaaagatatgttgatcaagtcattctt----gcagGTTATTGGAATCAATTTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTTCGACTTGCAATAATAGAATATA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
-gtttgttgcatctctcttgtgtgctttagatactacttttattgcttcctta-------------tttagttggtgactgaatta-tcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
| | || | | | ||| || | | | | | | | | | ||| | | | ||| | | | || ||||||||| ||||||||||| ||||||| || |||||||| |||||||| || |||||||||||| |||| ||||| ||||| |||||||| ||||| |||
cttatatttaagcctttatgtccgcataccacccgatactcacaaaatacaaagcaaaagaaaacttttggaagacattttaatcaatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 8
-----------gtttgt-tgcat-ctctcttgtgtgctttagatac-tacttttattgcttccttatttagttggtgactgaatta-tcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
| ||| ||||| | | | | | | | | ||| ||| | | ||| | | | || ||||||||| ||||| ||||| ||||||| || |||||||| |||||||| || |||||||||||| |||| ||||| ||||| |||||||| ||||| |||
ttatttaagccttatgtctgcataccaccctatactcacaaaacatgtacaaagcaaaagaaaacctttgaaagacattttaatcaatgtattcttgcagGTTATAGGAATCGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 7
------------------gtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
| || || || | || || || | | |||| || || | | ||| | | || |||||||||||||| ||||||| | || |||||| | |||||||||||||| || ||||| |||||| | || ||||| || |||||||||||||||||||||
tccatgacaagcttcagggctttaaagatgtc-catgcatgtgagaggagtcttatgtgcatgttcccctttcagacatt--ttaaataagcgattcttgcagGTTATTGGAACTGATCTATTGTCCCAATCCCTATTACCGGCCATTGTTGAGCTTGCAGAGGATAGACATTGGAGGGTTCGACTTGCAATAATAGAGTATAMapped 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|47830292|gb|CK119976.1|CK119976EST: TTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAG GTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAA
genomic: TTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgca ... tttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactacttttattgcttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
ttatctttt CT-rich tract
tgaattatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA