Sequence
atgc intronic sequence ATGC exonic sequencegcatgtacctctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13930.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
---------------------------------------------gcat-gtacctctgaatacctcttacgaaaattaacatggtttattgtttta--tcattctacta-aagatatctgttgaaa---cttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
|||| | | || | | | || | | | | ||| || | | | || | | | | || || || |||| |||||||| |||||| ||||||||||||| |||||||| | ||||||||||| ||||||||||| || |||
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 6
--------------gcatgtacctctgaatacctcttacgaaaattaacatggtttattgtttta--tcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
||| | | || | | | | || |||| | || | | ||| ||| ||| || |||| |||||||| |||||||||||||| ||||| ||||| || | ||||||||||| |||||||| || || |||
tgttttagttttgtacatattatgcaacttaattttccgcagcaacgcggcggggtattcatctagttagtattacaccttatacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTTTGTGAGGTGGAGACT
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------gcatgtacctct-gaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
|||| ||| |||| | | ||| || || | | ||| || | | | | ||| || |||| |||||||| |||||||||||||| ||||| ||||| || | ||||||||||| || ||||| || || ||
gtatctgttacgcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaccgttgctccttatctgtatttcttgaattgcatccatcggtgtta-cacctttaacaccagaagtattacaccttacacttgtattgt--ctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTCTGTGAGGTGGAGACG
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
gcatgtacct-ctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttgaaac-ttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
|| ||| || | ||||| || | | || || || | || ||| | || ||| | |||||||||||||||| || ||| |||||||||||||||||||| | |||||||||||||||| |||||||||||||||
----gttcctactattttaatcttatgagatt----gctgtatagtgggtcatgatttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
gcatgtacctctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatct--gttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
| ||| | | | ||||| || | | || || || | || ||| | || ||| ||| || |||||||||||||| || ||| |||||||||||||||||| | | |||||||||||||||| |||||||||||||||
gttcctacttttctgaa--tcttatgagatt----gctgtatagtgggtcatgatttctcctaaattattctcactgatacg-cagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
gcatgtacctctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttga--aacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
|||||| ||| | | || | | ||| | ||| | | | | | | | | | | || | | |||| | || | |||||||||||||| |||||| |||||||||| ||||||||| | |||||||||||||||| ||||||||||| |||
gcatgtgcctttctgaagctatga-gaatacaaaccatgctcaatttactgttttatgattgaatgt-tttgtttatcaaatgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACT
upper sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 6
gcatgtacctctgaatacctcttacgaaaattaacat---ggtttattgttttatcattctactaaaga--tatctgttgaaac--ttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
|||||||||| | | | | | | ||| | ||| | ||| | | | |||| | ||| | ||| | | ||||| || ||||| ||||||||||||||||| || |||||| || ||||||| ||||| | ||||||||||||||
gcatgtacctttagaagcattcaaaatcatttagattctgggtacaaagttgtctttgccaactagatgcttatgtattgttgccatgcagGGAAATATTGCGAGGTGGCTGAAGAAAGAGGGAGATAAAATTTCTCCTGGAGAAGTATTGTGTGAAGTTGAAACGMapped 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|124942142|gb|EL018433.1|EL018433EST: CTCCTCATCAAGAGATTGGAATGCCTTCTCTTTCGCCAACAATGACTGAG GGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTG
genomic: CTCCTCATCAAGAGATTGGAATGCCTTCTCTTTCGCCAACAATGACTGAGgcatgtacct ... gaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTG
EST:
gi|164199709|gb|ES187602.1|ES187602EST: CATCAAGAGATTGGAATGCCTTCTCTTTCGCCAACAATGACTGAG GGTAACATTGCCAGGTGGC
genomic: CATCAAGAGATTGGAATGCCTTCTCTTTCGCCAACAATGACTGAGgcatgtacct ... gaaacttcagGGTAACATTGCCAGGTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaacatggtttattgttttatcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
tactaaa putative branch site (score: 1)
tttattgttttatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgtacctctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatctgttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG