Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatctggctagtaatgttggttttggtgtttgattggaagcttatttgtttttctcatgattgttgacacatttgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G18950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G18950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G29520.1 (Glycine max), 3'ss of exon 2
----------------------gtaagaatctggcta--gtaat-gttggttttggtgtttgattggaagcttatttgtttttctcatgattgttgacacat-------ttgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
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gtgcgtgtgaatttaatattttcaaactatcaagttgtcgtatttatttgtcttgtcatgtaagttttagcttttgtattctgctggtgtttaccaatatttgttgtgattatactgtttcagATGGCCCCTATGCATGTTAATCATGCACGTGAAGTCCCAGAGTATGAAATCAATCCTAAAGAGCTTGATTTTACCAACAGTGTGGAGATAACAAAG
upper sequence: AT4G18950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G09490.2 (Glycine max), 3'ss of exon 2
--------------------------gtaagaatctggctagtaatgttggttttggtgtttgattggaagcttatttgtttttctcatgattgttgacacat-------ttgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
|| || || | | | ||||| ||| || | | | ||||| | | || | || ||||| | | || || || ||||||||||| || ||||| ||||| ||| ||||||||||| ||||||||||| ||||||| ||||||||||| || | || |||||||| |||
gtgcgtgtgaatttaggattttaattttattaagttgttttatt-tattggtcttgtcgtatcagttttagcttttgtattctgctggtgattaccaatatatattgtgattatactgtttcagATGGCCCCTATGCATGTTAATCATGCGCGTGAAGTCCCAGAGTATGAAATCAATCCTAAAGAGCTTGATTTTACCAACAGTGTGGAGATAACGAAG
upper sequence: AT4G18950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g02060.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------gtaagaatctggctagtaatgttggttttggtgtttgattggaag--cttatttgttt-ttctcatg------attgtt--gacacatt-----------tgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
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gtatgtcttggacttggttgtatatatatatggtgataagtgaactgtaattgctgattttgaagaagtatgtacagaccttagttgttggttctcgttgatagcatggtttggatttattcctttcctgtgtttttgtgtttagATGGCTCCCATGCATGTAAATAATGCCCGTGAAGTCCCAGAGTATGAAATTGATCCTAAGGAGCTTGATTTTACAAACAGTGTTGACATAACTAAGMapped 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|124860917|gb|EH945354.1|EH945354EST: ATACATGGAGCTAAACATCCG ATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATA
genomic: ATACATGGAGCTAAACATCCGgtaagaatct ... atgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattggaagcttatttgtttttctcatgattgttgacacatttgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
tgttgac putative branch site (score: 3)
tgttttc putative PPT
ttatttgtttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatctggctagtaatgttggttttggtgtttgattggaagcttatttgtttttctcatgattgttgacacatttgtatgttttcagATGGCTCCAATGCACGTTAAGACTGCTCGTGAAGTCCCTGAGTATGAAATAAATCCTAGTGAGCTTGATTTCACTCAAAGCAAAGAGATAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA