Sequence
atgc intronic sequence ATGC exonic sequencegtttgttacaacagaaatacccaaaccagatcatgccaatggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25800.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
gtttgttacaacagaaatacccaaaccagatcatgccaatggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
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--------------------------------agtcccacagctcaat-ataacatttcaattttg------cttccctaatgactgataaattccttggtcatagaaaattcattactgagtcct---tttgatcttt--cagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
---------------------------------------gtttgttacaacagaaatacccaaaccagatcatgccaa--tggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttat----atgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
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gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaa--gccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
---------gtttgttacaacagaaatacccaaaccagatcatgccaat--ggcttcatgataacatgttt-----tgtttaaaagactttcactcttttaacttgcctttctc---gcc---catccatattcag-------ttgatgacttctatattttat----atgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
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gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACAMapped 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|164172537|gb|EL996395.1|EL996395EST: CTTGACCAAGTGAATCAG GTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAA
genomic: CTTGACCAAGTGAATCAGgtttgttaca ... tatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAA
EST:
gi|164153443|gb|ES023314.1|ES023314EST: TCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGAATCAG GTTATTGGGATTGATCTAC
genomic: TCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGAATCAGgtttgttaca ... tatgtggcagGTTATTGGGATTGATCTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
agttgat putative branch site (score: 5)
acttctatattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttacaacagaaatacccaaaccagatcatgccaatggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA