Sequence
atgc intronic sequence ATGC exonic sequencegtgataactcatcagtttcttatagttatctgtctatcattgactttatttctccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G30970.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G30970.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 5
gtgataactcatcagtttcttatagttatctgtctatcattgactttatttctccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
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--------gtatagaaaggtgacaattgtcaatg-gtcatttgctatattgttttt--gccagttatagtagttctattttcttgatgcc-tttcagGTGAAGAAACATTTTCCATTCTTCGACATGGCATACCAAGGATTTGCTAGTGGTGATCCAGAGAGAGATGCCAAGGCAATTCGAATATTTCTTGAAGATG
upper sequence: AT2G30970.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 5
gtgataactcatcagtttcttatagttatctgtctatcattgactttatttctccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
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gtaatgggaactgaa---ctggggaacaaaaaagttgtatttcctgtgatcctac--aagccacacctaccagatttcactcttgttcctctat-agGTGAAAAAACATTTTCCATTCTTTGACATGGCATACCAAGGGTTTGCCAGTGGTGATCCAGAGAGAGATGCCAAGGCAATCCGAATTTTCCTTGAAGATG
upper sequence: AT2G30970.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
gtgataactcatcagtttcttatagttat-----ctgtctatcattgactttatttc--tccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
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-ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgact--ctttttcttgttcattgttatgattgt-ttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
upper sequence: AT2G30970.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 5
gtgataactcatcagtttcttatagttatctgtctatcattgactttatttctccttgatcagccctctgcagactaacatcgagttctcattt-cagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
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-------------------gtagacatagaagatgttcttttttttcagttctctgt-actgactttccatgttttaatacattatgatcattttcagGTCAAAGGTCATTTTGCCTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGACCCAGAGAGGGATGCCAAGTCCATCAAGATTTTCCTTGAAGATGMapped 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|86044680|gb|DR340435.1|DR340435EST: GAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTATTCAAG GCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGT
genomic: GAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTATTCAAGgtgataactc ... ctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGT
EST:
gi|116454920|gb|EG497512.1|EG497512EST: GAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTATTCAAG GCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGT
genomic: GAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTATTCAAGgtgataactc ... ctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttatttctccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
gactaac putative branch site (score: 1)
ttctcatttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgataactcatcagtttcttatagttatctgtctatcattgactttatttctccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG