Sequence
atgc intronic sequence ATGC exonic sequencegtatatatggaagcttttgactaacttgttgatcaaagatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G19420.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G19420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G17150.1 (Glycine max), 3'ss of exon 4
gtatatatggaagcttttgactaacttgttgatcaaag--atgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
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------gtattatcttctaatctatatattgtttctccttatgaactctaacaattttgct-tagcttt--ctaacgatttttataaacttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGGTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCAA
upper sequence: AT4G19420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08240.1 (Glycine max), 3'ss of exon 4
------------gtatatatggaagcttttgactaacttgttgatcaaagatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
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cattctgataccaaacgtatcacaatgtgtattatgtctatttatgagttgtgaactcaattgttttgcccagctttctaacgaaat----ttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCCA
upper sequence: AT4G19420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G17120.1 (Glycine max), 3'ss of exon 3
-----gtatatatggaagcttttgactaacttgttgatcaaagatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
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gtattgtccactagtcaatatgtattgtttctatttgtgagttgtgaactcaattgtttttgct-cagcttt--ctaacaaaatttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACTGGTGATGTGGAAGAAGTTGATCCA
upper sequence: AT4G19420.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08230.1 (Glycine max), 3'ss of exon 3
----------gtatatatggaagcttttgactaacttgttgatcaaagatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
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gcagcatcattctgatacaaaacgtatcacaatgtgtattgtttctatttgagttgtgaattgttttgctcagcttt--ctaacgaaatttataaatttcagATTTCTACAATTGGAATAGAGTCAAGGTTAGGTACTGTGATGGTTCATCGTTTACCGGTGATGTGGAAGAAGTTGATCCAMapped 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|86031811|gb|DR327564.1|DR327564EST: GAACCTTGCTTTCTCAGCTATTCTTAGCAATAAGAAACAATATAATCCTG ATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCAT
genomic: GAACCTTGCTTTCTCAGCTATTCTTAGCAATAAGAAACAATATAATCCTGgtatatatgg ... gaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCAT
EST:
gi|86031812|gb|DR327565.1|DR327565EST: GAACCTTGCTTTCTCAGCTATTCTTAGCAATAAGAAACAATATAATCCTG ATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCAT
genomic: GAACCTTGCTTTCTCAGCTATTCTTAGCAATAAGAAACAATATAATCCTGgtatatatgg ... gaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
ttaagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatggaagcttttgactaacttgttgatcaaagatgaagttaagtttttgtcttatgggtttggttggttcttcttggaaatggcagATTTTTACAATTGGAATAGAGTGAAAGTTAGATACTGTGACGGGGCATCATTCACAGGAGATGTAGAAGCAGTGAACCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC