Sequence
atgc intronic sequence ATGC exonic sequencegtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g10850.1 (Oryza sativa), 3'ss of exon 2
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcactta---tgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
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--------------------------------------------------------------------------------------cccatgccatacattgctattctaagcgctgttctgctaggtttctgagtagactatattttcatatgtcctaagtcccaatccatacttctgc-tttcagCTTAAAGAGCTTGAGAAGTTGGGTCCCAAAAAGGGTGTCATCAGTCAGTCAGTGAAGGATGTTGTGCAAAGCCTGGTGGATGATGATCTTGTCTTGAAAG
upper sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G102242_T02 (Zea mays), 3'ss of exon 2
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
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----------------------------------------------------------------------------cagattttgctac-tgtagcttctgttctgttaagttttgtca-tgtagga--tgtgtttttccgatgccatagaatataattcttaccatatgctat----ttttagCTTAAGGAGCTAGAGAAAATGGGTCCTAAAAAGGGAGTGATTAGTCAGTCTGTGAAAGATGTGGTGCAAAGCCTGGTGGATGATGATCTTGTCTTGAAGG
upper sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
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------------------------------------------------gtaatcaccatta-ctatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgact----gatttatgtgctttttgtttttggtttttttttttcg---gttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
upper sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g02770.t01 (Vitis vinifera), 3'ss of exon 1
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatc-tagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
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------------------------------------------------------------------------agcccatatcatacagacttggatggccttcaggaattaaaagtactgttttc-----ttagtgagaataatgtat-cactgatacgt-------tttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAGMapped 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|164055692|gb|ES087861.1|ES087861EST: GATATTCTATGAGTCTCAAGACTTCTTCCTA CTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCT
genomic: GATATTCTATGAGTCTCAAGACTTCTTCCTAgtgagcactt ... aaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCT
EST:
gi|152033982|gb|AU238562.2|AU238562EST: AACGAGAGAAGATGCTTCAGATATTCTATGAGTCTCAAGACTTCTTCCTA CTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCT
genomic: AACGAGAGAAGATGCTTCAGATATTCTATGAGTCTCAAGACTTCTTCCTAgtgagcactt ... aaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
tctacttttgtaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG