Sequence
atgc intronic sequence ATGC exonic sequence...cactaccaccccctcctgtctatcgtctgctttatttggtttacagtttttcagcttcacagtagaatatttgattcgttttttttttaattatttgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAAGACGATTTAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 2
cactaccaccccctcctgtctatcgtctgctttatttggtttacagtttttcagcttcacagtagaatat----ttgattcgtttttttttta--attatt--tgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAA---GACGATTTAGTG
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------gaatttattcaattca-catcccatttgctcc-tatatatgctgtcagtgccatgttaaatgatgattcttactagttttctcttaaaaataattcatgcagACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 2
cactaccaccccctcctgtctatcgtctgctttatttggtttac-agtttttcagcttcacagtagaatatttgattcgttttttttttaattatt--tgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAA---GACGATTTAGTG
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--tcacatcccatttgctactat-atatgctctcagtgccatattaaatgatgaaattcttattagtctagtttgatttttctcgtaaaaacaattcatgcagACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 2
cactaccaccccctcctgtctatcgtctgctttatttggtttacagtttttcagcttcacagtagaatatttgattcgtttttt---ttttaatta--tttgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAA---GACGATTTAGTG
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----gtggttttctcctacctatatactgcaagagggagctggtggttttcttattt-ggaggaataagttcatcttttttttggggtataaaatggttttgcagACAGAGAAAATAGAACTGGAAACTACTGTAGTGGATGAAACAAAGGAACGGGAGTCATACTGTGGCCAAGGAAATAGAAGATTCAGTGMapped 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|164116361|gb|EL987001.1|EL987001EST: TGGATACACTGAGACAGTTAGAG ACTGAG-AAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCAT
genomic: TGGATACACTGAGACAGTTAGAGgtatgtttta ... ttatttgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttcagcttcacagtagaatatttgattcgttttttttttaattatttgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAAGACGATTTAGTG
ttttaat putative branch site (score: 3)
ttttttttttaatt CT-rich tract
agtagaatatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactaccaccccctcctgtctatcgtctgctttatttggtttacagtttttcagcttcacagtagaatatttgattcgttttttttttaattatttgcagACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAAGACGATTTAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA