Sequence
atgc intronic sequence ATGC exonic sequencegtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttggtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G37500.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 8
gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttggtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
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-tttggtttcttaatctttgaaaagtatatagctctgaacaacacttgctgtgtctacttttcattccttttttcatcaaatcttattagcttgcattcagGGCAGATTCTGCAGCTGTGGCAATCACCACTACAGATCTTGTTAGCAAGAGTGTGGCAATTGAGTCTCTG
upper sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 7
gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttggtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
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-tttagtttcttaatctttgaaaagtatatatctctgaacaacacttgctgtctctacttttcaatcctttgttcatcaaatcttattagcttgcatacagGGCAGATTCTGCAGCTGTGGCAATCACCACGACAGATCTTGTTAGCAAGAGTGTGGCAATTGAGTCTCTG
upper sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 8
gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttggtagcc-attggg-cat-----aaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
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----tttttgggcatcttgatatttctttttgattgatc--cctttgtcttc-ttttctgtactattttattgaaacattcttgaatcttatatctgg-ggattgcagGGCAGATTCTGCAGCAGTAGCTATTACCACAACCGACTTAGTGAGCAAGAGTGTGGCAATTGAATCTGAG
upper sequence: AT2G37500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S90_220V6.1 (Physcomitrella patens), 3'ss of exon 9
-----gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttg-gtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
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gatggacatgggcttgtgt-catggtggtttcttcagacgctagaatcac----ttgggtatgtatgtatggcctatgtggatattgatgggaatttct--ttgcagGGCTGATGCCGCAGCCGTAGCCATCACAACTACTGATCTTGTCAGCAAGAGTGTTGCAATTGAAACGAAGMapped 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|124842789|gb|EH927226.1|EH927226EST: CTCTAGTCAACTCGAGATCAGACTCTGTGGAAGA GGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAANCAAG
genomic: CTCTAGTCAACTCGAGATCAGACTCTGTGGAAGAgtataatctt ... tgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAG
EST:
gi|124787522|gb|EH877201.1|EH877201EST: CTCCACGCACTTCCAACTCTAGTCAACTCGAGATCAGACTCTGTGGAAGA GGCAGATTCTGCTG
genomic: CTCCACGCACTTCCAACTCTAGTCAACTCGAGATCAGACTCTGTGGAAGAgtataatctt ... tgaaatgcagGGCAGATTCTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttcactttctttggtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
gcataac putative branch site (score: 3)
atatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatcttcttttctcaatctctcttttaagttcgtaggtcacagtcttcactttctttggtagccattgggcataaccatatgaatgttgaaatgcagGGCAGATTCTGCTGCTGTAGCTATCACAACAACAGATCTTGTAAGCAAGAGTGTTGCAGTTGAATCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA