Sequence
atgc intronic sequence ATGC exonic sequence...ttactgttcactgattcatgttctgttacatcttttggttggtgattttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60970.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
----ttactgttcactgattcatgttctgttacatcttt--tggttggtgat--tttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
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ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcac--------agGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
----ttactgttcactgattcatgttctgttacatcttttggt--tggtgat--tttcaatatctcttaatcttt-------attctattctgtgtttt-cattacttacattt---agGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
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gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
ttactgttcactgattcatgtt---ctgttacatcttttggttggtgattttcaatatctcttaatct--ttattctatt--ctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
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-------aaacaaattcaaatttatcattcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgatatttatgtaattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
ttactgttcactgattcat-gttctgttacatcttttggttggtgattttcaatatctcttaatct--ttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
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--aacgggcatcgaggctttgtactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctgg-atgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATAMapped 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|152034836|gb|BP837875.2|BP837875EST: TTTCTTTATTACTAGGGCATTCTCTGCAGATTTCTTCTCCTTAAGCCATG GAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAG
genomic: TTTCTTTATTACTAGGGCATTCTCTGCAGATTTCTTCTCCTTAAGCCATGgtatgaatct ... ttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
tacttac putative branch site (score: 1)
ttaatctttattctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttactgttcactgattcatgttctgttacatcttttggttggtgattttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- -ctgttca
- - - - - ctgattc
- - - - - - - - - - - ctgttac