Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G31070.1 (Glycine max), 3'ss of exon 1
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
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gtaactctctttcct------tctctctattttctcctcttttgctt--ctcgattttactg---ttttgccactga----tcggtgcggttgat--gcttgttcctcgcggatc-gcagCAAATCGAAGCTTTACCGGTTCGACAAGGATGGGAACCAGTGGAAGGAGCGAGGCGCGGGCACCGTGAAGTTCCTGAAGCATAAGGCTACGGGCAAGGTT
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
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gtaacgctctttctt--------tctctcgtttttctccttttttgcttcccgattttactg---ttttgccactga----ttggtgcggttga-tgcttgttttctcgctgatc-gcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g06880.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
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--------------------------gtaattctctcctcttagatcagt--atctccattttttcccttgattctagggttt--tgttcttgattgtact---------ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAGAGGTGCTGGTAGTGTGAAGCTTTTGAAGCACAAAGAATCTGGCAAGGTC
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0217g00030.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
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------------------------gtacagttactttg--ttaaattctagggtttttattga-----tgatctctagggttt----tctctgattggttgttaatcggagtgtttta-gGAAAGCAAAGCTTTATCGATTCGATAAGGAAGGGAAGCAATGGAAAGAAAGAGGCGTTGGAACTGTGAAGTTCTTGAAGCACAAAGGGTCGGGCAAAGTTMapped 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|124716203|gb|EH807605.1|EH807605EST: TGCCGTCCTTGATCT GAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAG
genomic: TGCCGTCCTTGATCTgtaagtgttt ... gaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAG
EST:
gi|164087606|gb|ES066084.1|ES066084EST: TCACTACCGGCGAGGAAGACGAAGATGCCGTCCTCGATCT GAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAG
genomic: TCACTACCGGCGAGGAAGACGAAGATGCCGTCCTTGATCTgtaagtgttt ... gaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
gtttgac putative branch site (score: 4)
aatttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA