Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21160.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G161728_T04 (Zea mays), 3'ss of exon 3
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgctt----attacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
|| | ||| || |||| | | | || || || ||||| || |||| || | | ||| ||| || || ||| || ||| ||| || |||||||||||||||||| | |||||||||||| | | ||| || || ||||| | | |||||||||
----------------------------------------------------aacaaaaatgaatgcccaatatg--cacagtactttattt-tg---tttttatttcatttcattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 3
gtaagttttgccattttt---atgttttgttccagtaagcat---tttatgcttctctaagcagtttgattgaatgtt-atgatcttgtttccctact-tgtgcattttttggtttgtttcgtttttcgtaaacccataaa---actcttggttgct-tattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
|||||| || ||||| | || ||| ||| || || | || || ||| | |||| ||| || || | | | | |||| | | | ||| | || ||| || | || || |||||| || || |||||||| |||||||||||||||||||||||||| |||||||||||||| | |||||| ||||||
gtaagtgtttaattttttcacacgtgacgttgtggtatatattaattggcattatcatacttttttcgatgaactgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaagaacgtgtgaattcacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 1
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgat--tgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
|||| || | | | | || || | | | || | || ||| || | || || |||| | | ||||| || ||||||||| ||||||||||| ||| |||||||||||||||||||||| |||||||| |||||| ||| || ||||||
---------------------------------------------------taagttgtagggtaatagctacatgaattttcctaaattgataatgtggaatgcatattacttc-ttagttgtgaatccatt---tttctaactgcttctt-cagGTCAGCCAATATTGGAGTTTTTGTATGCTTAAAATGTTGTGGTGTGCACAGAAGTCTTGGCTCTCAAATATCAAAG
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 3
gtaagt-tttgccatttttatgttttgttccagtaagcattttat---gcttctctaagcagttt--gattgaatgtt-atgatcttgtttccctact-tgtgcattttttggtttgtttcgt-ttttcgtaaacccataaa---actcttggttgct-tattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
|||||| ||| |||| | | | | || ||| || | | | ||| | | | |||| ||| || || | | | | |||| | | || ||| | || ||| || | || || |||||| || || |||||||| |||||||||||||||||||| ||||| |||||||||||||| | |||||| ||||||
gtaagtgtttaattttttcacgcatgactttgtggtttatattaattggcattatcatactatttttggtgtagtgtttgtgaatatgacataaagctgtaggaaactagctacttgtaaaatatattaaagaacatgtgaattaacttttactaactgcttttcagGTCTGCCAACATTGGAGTTTTTATATGCTTAAAATGTTGCGGTGTGCACAGAAGCCTTGGTACTCATATATCAAAG
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 1
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgat-tgaatgttatga-tcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
|||| || || | |||| | || | | | || | || || || | || || |||| | | ||||| || ||||||||| ||||||||||| || ||||||||||||| |||||||| |||||||| |||||| ||| || ||||||
---------------------------------------------------taagttgtaggaaactagcaacatgaattttcctaaaatgataatgtggaatgcatattacctc-ttagttgtgaatccatt---tttctaactgcttctt-cagGTCAGCCAATATTGGAGTTTTCGTATGCTTAAAATGCTGTGGTGTGCACAGAAGTCTTGGCTCTCAGATATCAAAG
upper sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
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-------------------------------------atttgaca--tccacacacaaatccgtttaatgt---agctgtgaattcatgt---tgttttcttcagcatatgcttatatatgtgtacttgaacaatgcat---------tttcagGTCTGCAAATATTGGAGTCTTTATATGCTTAAAATGTTGTGGTGTGCACAGAAGCCTTGGTACACATATCTCAAAGMapped 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|125090685|gb|EL148577.1|EL148577EST: ATCCTAAGTGGGC GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAG
genomic: ATCCTAAGTGGGCgtaagttttg ... cttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAG
EST:
gi|164236042|gb|EL968084.1|EL968084EST: AGTCTGCGCTGATTGTGGCGCTCCAGATCCTAAGTGGGC GTCAGCTAATATTGGAGTGTTTATATGCTTAAAAT
genomic: AGTCTGCGCTGATTGTGGCGCTCCAGATCCTAAGTGGGCgtaagttttg ... cttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
ataaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgcttattacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC