Sequence
atgc intronic sequence ATGC exonic sequencegtagttaacaaaatccttctcatctatctgcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51460.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G36570.1 (Glycine max), 3'ss of exon 9
gtagttaacaaa---atccttctcatctatctgcttctgttctgaatcttggt---ttggtttg--gccattgacttta---atac-atttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
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gtgagttccgtttttgtttttttaatatggtttctttttttaatgatcacagtacattgttttgcagtaactgatattagacatattgttttttagGGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCGGACAGACGAAGATGCATTTAAG
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 9
gtagttaacaaaatccttctcatctat--ctgcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAAC--AACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
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---gtgagttcattgtttttagttaatggttactttctttgaagatcagaattttgttatggagcaaatgacataagacttcttcatctagGACTTAATTGTGATGACGTGCTCGCTATTTATGTTGGGGATGATAGAACAGATGAAGATGCATTTAAG
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 9
gt-agttaacaaaatccttctca-tctatctgcttctgttctgaatcttggtt--tggttt---ggccattgactttaat--acatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
|| |||| | | || | | | || | ||| | || ||| ||| | |||| | | |||| ||| ||| | ||| |||||||| ||||| ||||| ||||| || ||| |||| ||||||| || ||||||||||||||||||
gtgagttcattttttgttttttagtatagtttctttttttaatgatcacagttcattgttttacagtaactgacattaggcattgttttttagGGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAG
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ22626 (Selaginella moellendorffii), 3'ss of exon 6
gtagttaacaaaatccttctcatctatctgcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
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-------------------gtaagtgtttgctacttttttg----ttgaa--gatgcgatctttaaacttctttggttg--aagGCCTAGGCGACAGCCGAGATGTTCTGCCGGTCTATATTGGGGATGATCGAACGGACGAAGATGCGTTTGAG
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ11784 (Selaginella moellendorffii), 3'ss of exon 6
gtagttaacaaaatccttctcatctatctgcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
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-------------------gtaagtgtttgctatttttttg----ttgaa--ggtgcgatctttaaacttctttggttg--aagGCCTAGGCGACAGCCGAGATGTTCTGCCGGTCTATATTGGGGATGATCGAACGGACGAAGATGCGTTTGAGMapped 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|47828165|gb|CK117849.1|CK117849EST: GATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCG GCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAA
genomic: GATTGACTGGGACAAAGGGAAAGCTGTGACATTTCTACTTGAATCACTCGgtagttaaca ... catttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
catttctc CT-rich tract
actttaatacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttaacaaaatccttctcatctatctgcttctgttctgaatcttggtttggtttggccattgactttaatacatttctcagGCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG