Sequence
atgc intronic sequence ATGC exonic sequencegtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgctcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46290.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 5
gtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctg---ctctcgctct---tttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG----
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ttcatcattgatagtaccctatgaacatctttgac-cttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGGTAA
upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
gtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctc---gctcttt---tagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
| || | || | | | || || | | | | | | | || | || |||| |||||| || | || | ||||| || |||||||||||||| |||||||||||||| ||||| ||||||||||||||||| || |||||||| || || || |||| |
ttcatcattgatagtaccctatgaacatctttgac-cttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 2
gtatgcactaa---tgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctct-cgctcttt---tagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
|| | ||| || || | | || |||| | | |||||| | | || | | | ||| || || | |||| || ||||||||||||| ||||| |||||||| || || ||||||||||||||||| || |||||||| || || | |||| |
--ataaaataaatgccctcctatatgcttttgtttccttccatgttttatttgggtgatatgttacttgtatggttttctgaattctatgccctgtgtgcagGTGGTTATTGGAGGTGGTCAGGATGCGTCAGCTGTTACAACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTTTGACAAG
upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 2
----gtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgctctttt--agGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
||| | || ||||| | | | || |||| | | ||| | | ||||| | | | ||| ||| | |||| || ||||||||||||| ||||| |||||||| || || ||||||||||||||||| || || ||||| || || | |||| |
caaaatatttcatcat-cttctatatgctttagtttccttccatgttttatttgggtgatatgcgacttgtgtgattttctgaattctataccttgtgtagGTGGTTATTGGAGGTGGTCAGGATGCCTCAGCTGTTACAACTACTGATCATCGTGCTGGCAAATTCGAAGCCAAATTCTTTGACAAG
upper sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
-gtatgcactaatgct---tcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgc-tcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
|| || || | | | ||||| | | ||| | | | | ||| | | || || || | || | | | | |||| || || ||||||||||||||||||||| ||| || || ||||||||||||||||| |||||||| || || || || || | |
tatacttacatgtgttgggtatataaatttacagatggtggaaatagatatcgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGMapped 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|116426847|gb|EG469439.1|EG469439EST: CCACTGTGGTGCCTGTAAATGCTGTCGCCATGTCTCCACTTCTCAACCAT GTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCAT
genomic: CCACTGTGGTGCCTGTAAATGCTGTCGCCATGTCTCCACTTCTCAACCATgtatgcacta ... gctcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCAT
EST:
gi|116426850|gb|EG469442.1|EG469442EST: CCACTGTGGTGCCTGTAAATGCTGTCGCCATGTCTCCACTTCTCAACCAT GTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCAT
genomic: CCACTGTGGTGCCTGTAAATGCTGTCGCCATGTCTCCACTTCTCAACCATgtatgcacta ... gctcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgctcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
tcttgat putative branch site (score: 4)
tgtttctgctctcgct putative PPT
ttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctcgctcttttagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC