Sequence
atgc intronic sequence ATGC exonic sequencegtatcataacaccgtttccatatgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------gtatcataacaccgtttccatatgaattcagcttcaaaaggttcgagctttccat-tgttagttttacgccaaact---aattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
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gtatgttttttttttccaacttgttataaatgaccagaacgtgcatgattcatgaagctttgttataagggatctgctcgt-tcggaatgtagtcttt-tagcagtcatagatcatagtccttctgctccatgtctgctagtttt-cactaaacttttgctttttgaacgtatttcagGTAAATAACACTGACGCAGAAGGAAGGCTAACACTTGCTGATGCTTTGGTCTATGCTTGCAACCAAGGTGTTGAAAAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G178958_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------gtatcataacaccgtttccatatgaattcagcttcaaaaggttcgagctttccat-tgttagttttacgccaaac---taattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG----------------------
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gtatgttttttttttccaacttgttataaatgaccagaacgtgcatgattcatgaagctttgttataagggatctgctcgt-tcggaatgtagtcttt-tagcagtcatagatcatagtccttctgctccatgtctgctagtttt-cactaaacttttgctttttgaacgtatttcagGTAAATAACACTGACGCAGAAGGAAGGCTAACACTTGCTGATGCTTTGGTCTATGCTTGCAACCAAGGTGTTGAAAAGGTAATGAAGCTTCATTTGGAAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
gtatcataacaccg-tttccat-atgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtatt----gcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
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ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgttt-ttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 6
gtatcataacaccg-tttccat-atgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtattgc----agGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
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taattggagttttggccttgatgatttatttaatataacatgtgtagtactttaccccgttc-ttgtactgaggatttgataggcttaacatcttccctagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 6
gtatcataacaccg-tttccat-atgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtatt----gcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
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taattggagttttggccttgatgatttatttaatataacatgtgtagtactttaccccgttc-ttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 6
gtatcataacaccgtttccatatgaattcagcttcaaaaggttcgagct---ttccattgttagtttt--acgccaaactaattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
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agtccattttgttaagtccatggagaaactgattgattgcatatgtgttatgtttatttatgaattcctaatgtgttgttggctcccatctctactgcagGTCAATAACACAGATGCAGAGGGCAGACTCACACTTGCAGACGCTTTGGTATATGCTTGTAACCAAGGTGTAGAGAAGMapped 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|124952588|gb|EL027846.1|EL027846EST: GAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG GTACAACAACAC
genomic: GAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAGgtatcataac ... ggtattgcagGT-CAACAACAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcgagctttccattgttagttttacgccaaactaattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
aactaat putative branch site (score: 2)
ttagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcataacaccgtttccatatgaattcagcttcaaaaggttcgagctttccattgttagttttacgccaaactaattgtgggtggtattgcagGTCAACAACACCGATGCTGAAGGTCGACTAACACTTGCAGATGCTTTAGTTTATGCTTGCAACCAGGGTGTCGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG