Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21160.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
-------------gtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
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aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaatatgacacttcatgttatcaattgtctgtt---gcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 8
-----------gtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
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ttccctattctctctgtgtgtgtctgtacatgggaaagaagataactgatttttggtttgagaatatgacacttcatcttatcaattgtctgtgct-gcagAAAGTATTTGATCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 6
------gtaaaagcttgg-tctaatatttccaaaatcactttctactcttga----tgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
| | |||| | | | | ||||| | ||||| | | | |||| | ||| | | || ||||||| || || |||| | || ||||| |||||| ||||| ||||||||||||||||| ||||| || |||||| | ||||| ||||| ||||| ||||| || | |||||
ttgtctctctgtgtttggatacagaagatacaaaactaatttctggtgtaaaaacatgaaactttattctaatggtttggttacattaattgcatt-gcagAATGTATTTGATTATGACTTGTTTTCGGCTGATGACATAATGGGGGAAGCAGATATTGATCTTCAGCCGCTGATAACATCCGCAATAGCATACGGAGATG
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------------------------------gtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttccc--ttacattttatgttt--ttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
| | | || | | || | | | || | | || || | | | || ||| ||| | | ||| || |||||| | || ||||| |||||| ||||| ||||||||||||||||| ||||| || |||||| | ||||| ||||| ||||| ||||| || | || ||
gtaagattgaatttcatcttgtattgttagaaaatggaaacaaattctgtgatgcttattcggtgtttggatatttggatcttcatgtgtgatacttctatttgtctgtatgtgtgttttggtacagaagatacaaaattg-atttctggtgtaaaaacatgtaattttatcctaactgctggttacattgcattgcagAATGTATTTGATTATGACTTGTTTTCGGCTGATGACATAATGGGGGAAGCAGATATTGATCTTCAGCCCCTGATAACATCCGCAATCGCATACGGTGATG
upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaagcttggtctaatatttccaaaa--tca--ctttctactcttgatga--atcattacagaagtttttcccttacatttta----tgttttt------gcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
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------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATGMapped 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|86075296|gb|DR371053.1|DR371053EST: ATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG CAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCT
genomic: ATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTGgtaaaagctt ... gtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
cccttac putative branch site (score: 3)
tgttttt putative PPT
ttacattttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagcttggtctaatatttccaaaatcactttctactcttgatgaatcattacagaagtttttcccttacattttatgtttttgcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA