Sequence
atgc intronic sequence ATGC exonic sequencegttgctacaacttctaactcacctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G20410.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
-------------------------------gttgctacaacttctaactc--acctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
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gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttagttttctggttgctctttctag-taatccactggtatatgtttaata-----gGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
upper sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------gttgctacaacttcta-actcacctcattat---cattcttgaaagatgggcaagttttaa-----attttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
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gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaa-aatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
upper sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ27746 (Selaginella moellendorffii), 3'ss of exon 13
gttgctacaacttctaactcacctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
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-------------------------gtgcagactcaaagttggttctttgcgtttactatctcagctttctagGCTGGAACATACGTTAAGGAGTTTGTTCACGGAGATCTAGGACGAACGTATCCGAA
upper sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ37198 (Selaginella moellendorffii), 3'ss of exon 9
gttgctacaacttctaactcacctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
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----gtgcagactcaaagttggttctttgcgttt------------acaacgctaactatctcagctttctagGCTGGAACATACGTTAAGGAGTTTGTTCACGGAGATCTAGGACGAACGTATCCGAAMapped 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|19800018|gb|AU231308.1|AU231308EST: AAAAGATAAAAGGACACTCTCACTACTTTCTATTGCATCTGTGCACCCAG GCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACT
genomic: AAAAGATAAAAGGACACTCTCACTACTTTCTATTGCATCTGTGCACCCAGgttgctacaa ... aataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
aagttttaaattttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgctacaacttctaactcacctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC