Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggacaaagagttacaaacttttaataatagtctttcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtggacaaagagttacaaacttttaataatagtctt----tcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
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gtttgaaatgattcacctttctgattatagaacttatctagttgttgtaaataattctagcttaatcttggaac-tggttgttgatagGTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG
upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ12424 (Selaginella moellendorffii), 3'ss of exon 6
gtttgtggacaaagagttacaaacttttaataatagtctttcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
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-------------------------gtaagtcttccactttcaa--gtaacctgtgattgaatctggcg---tgtaaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATGGGTGGGAAGCCGCTGTACGAGAATCCCTTCTACACGGCTCCAAACATGMapped 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|164214022|gb|ES092338.1|ES092338EST: AGTCAGATAAAATTGCAAAAGGTGGCCTGGATAAAATGACCCTTATCGAG GTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGA
genomic: AGTCAGATAAAATTGCAAAAGGTGGCCTGGATAAAATGACCCTTATCGAGgtttgtggac ... ttgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatagtctttcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
tattgac putative branch site (score: 2)
tttttgattgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggacaaagagttacaaacttttaataatagtctttcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG