Sequence
atgc intronic sequence ATGC exonic sequencegtagtctcttaatcctttcaatcattagtaaaaatcttttagtgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02560.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
gtagtctcttaatcctttcaatcattagtaaaaatcttttagtgaagtcttatgaatttca-tttttctgatgtgagtcatgctttattcgtaaa---actgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
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--------gtaccagtagtgattgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G01510.2 (Glycine max), 3'ss of exon 7
--------------------------------------gtagtctcttaatcctttcaatcattagtaaaaatctt--ttagtgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
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gtattcttttaacatgcaatcagtgtatccatccccctatcccctctctctttctttgttgatgaatgtcattttcacctctcgaaaataagaaaaatgcttctttctaactttatatcccttcctctttcacttctgaagGAAAGAGATACAGCTTGCCAAATTCAAGGATAATGATTCATCAACCGCTTGGTGGTGCTCAAGGAGGGCAAACTGACATAGATATTCAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G01550.2 (Glycine max), 3'ss of exon 7
------------------------gtagtc-tcttaatcctttcaatcattagtaaaaatcttttag------tgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
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gtattcttttaacatgcaatcgctgtatctatccccccctctttctttgttgatgaatgccatttccacttcttgaaaattagaataatgcttctttctaactttatatcccttcctccttcacttctgaagGAAAGAGATACAGCTTGCCAAATTCAAGGATAATGATTCATCAACCGCTTGGTGGTGCTCAAGGAGGGCAAACTGACATAGATATTCAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 7
-------------------------------------------gtagtctcttaatcctttca-atcattagtaaaaatcttttagtgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
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gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 7
----gtagtctcttaatccttt-caatcattagtaaaaatcttttagtgaagtcttatgaatttcatttt--tctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
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gtaagtaatttcctaggcttttgttgttagtggtttggagttccacttcgtggcatatgctttttggtgtgctttgacatgtgtctgtcacctccctcttaactgaagGAAAAAGATATAGCTTGCCAAACTCAAGGATCATGATCCATCAGCCTCTCGGTGGAGCTCAAGGTGGGCAAACTGACATAGATATTCAGMapped 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|124790523|gb|EH880202.1|EH880202EST: TATGGGAGCTTTTCTGCTTAGTGCTGGAAACCAAAG GAAAAAGATACAGT
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGAA-CCAAAGgtagtctctt ... aaaactgtagGAAAAAGATACAGT
EST:
gi|125100100|gb|EL155679.1|EL155679EST: TATGGGAGCTTTTCTGCTTAGTGCTGGAACCAAAG GAAAAAGATACAGT
genomic: TATGGGAGCTTTTCTGCTTAGTGCTGGAACCAAAGgtagtctctt ... aaaactgtagGAAAAAGATACAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
ttctgat putative branch site (score: 3)
atgaatttcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtctcttaatcctttcaatcattagtaaaaatcttttagtgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA