Sequence
atgc intronic sequence ATGC exonic sequence...tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctcttctaatatctgaagctttaatcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 3
tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctcttctaatatctgaagctttaatcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
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----------------------gttggaaaattttccttcagacctcttgttgtctatcagttgttctattttaaacgttt-----cttttctgttgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCAGAGTTCATGACAAATACAAAATTAGCAATAA
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 3
tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctc--ttctaatatctgaagc-ttta-atcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
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-----------------------------------gttagtgatttcttctagacatcctgttgtctcttagtgcatctatctgaatcatttatattctcgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCGGAGTTCATGACAAATACAAAATTAGCATTAA
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 3
----------------------------tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctcttctaatatctgaagctttaa---tcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
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gtaagattttctactacatcacttgcacgggagaaatatagttctataat-ctcagtgattgcactcc----tgttcatctgttatgcagttttggtaatatactttaataaattttaaaattccatacagGTCATGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAATTTTTTGACAGATGCCAAATTGGCTATAA
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 4
tagcaatatgcgttcatataatactcaga-aacagaatcatagattgttgact----tgatctctatt--tttcctcttcta---------------atatctgaagctttaa--tcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
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--gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAAMapped 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|116416941|gb|EG459533.1|EG459533EST: AGCTTCCACTATTGAAGGCCAAGCAGTTTGCATGTTTGGAATATTTGATG GCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACA
genomic: AGCTTCCACTATTGAAGGCCAAGCAGTTTGCATGTTTGGAATATTTGATGgttagattct ... atcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgacttgatctctatttttcctcttctaatatctgaagctttaatcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
tctattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagcaatatgcgttcatataatactcagaaacagaatcatagattgttgacttgatctctatttttcctcttctaatatctgaagctttaatcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - -cagaaac
- - - - - - - - - - - - - - - - - aatcata