Sequence
atgc intronic sequence ATGC exonic sequencegtaagattcgtttcttatcccttgcttttaaactcataacacagctggtactgatcttgtatgttatgacgttttggcagGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTTGTGGAGCATTTTTTCCTAGTTAATCACCCTGATAACTACCTCACACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 3
-------gtaagattcgtttcttatcccttgcttttaaactc-ataacacag-------ctggtactgatcttgtatg---ttatgacgttttggc--agGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTTGTGGAGCATTTTTTCCTAGTTAATCACCCTGATAACTACCTCACACATC
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gttgtagacgggaatggtttcatatctcaattgaataaacacgatgagttaatttccttctggttggtttgttgaatgcacctcaaatgatttattttagGTTCTTGTGCGGAATATACCTCCAGATCCTGATGAATCAATTAGTGAGCTCGTGGAGCATTTCTTCCTTGTTAATCATCCTGATCATTATCTAAGACACC
upper sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gta-agattcgtttcttatcccttgctt-ttaaactcataacacagctggtactgatcttgtatgttatgacgttttggcagGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTTGTGGAGCATTTTTTCCTAGTTAATCACCCTGATAACTACCTCACACATC
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ttcatttaggtttactagttatacagctccaaattatatattttcatgattccttccttttcattgcca-tgtttgtgtaatggattttggt-tatttgcagGTCCTTGTTAGGAATGTGCCCCCAGACGCAGATGAATCTGTTAGTGAGCTTGTGGAGCATTTTTTCCTGGTCAATCATTCAGATAACTATCTTACTCATCMapped 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|125089334|gb|EL147742.1|EL147742EST: AAGGCCGTCGACCTGACCAGTTCACT GTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTT
genomic: AAGGCCGTCGACCTGACCAGTTCACTgtaagattcg ... gttttggcagGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaactcataacacagctggtactgatcttgtatgttatgacgttttggcagGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTTGTGGAGCATTTTTTCCTAGTTAATCACCCTGATAACTACCTCACACATC
tactgat putative branch site (score: 2)
tatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattcgtttcttatcccttgcttttaaactcataacacagctggtactgatcttgtatgttatgacgttttggcagGTTCTTGTTAGGAATGTACCTCCGGACCCAGACGAAACTGTGAGTGAGCTTGTGGAGCATTTTTTCCTAGTTAATCACCCTGATAACTACCTCACACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA