Sequence
atgc intronic sequence ATGC exonic sequencegtgagacgattctatatttctatgaaaggatacagtttttcacttttcttcctgtttaaaattcttactggttgcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTTTCCACTGCAGTAGCCAAATGGGATGCAGAGTTCTATATCAAGGTAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77810.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------------gtgagac--gattctatatttctatga--aaggatacagtt--tttcacttttcttcctgtttaaaattcttactggttgcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTTTCCACTGCAGTAGCCAAATGGGATGCAGAGTTCTATATCAAGGTAGATG
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gtatggtgacatccaccaaaagtagaagcacatcattctttacctatttctgttaaaccaaaatctgttttactgtgattggggctgtagtccatactaatgtttattctgctgcaaccacaca-tgtatgtagGACCATGTTGAAGGGTATCACGAGCTATCTGCAAAGACCAAGATATTCTTTTCCACTGCTGTGGCATTATGGGATGCTGATTTCTATGTCAAGGTGGATG
upper sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 6
gtgagacgat--tctatatttct-----atgaaaggatacagtttttcacttttcttcctg--tttaaaattcttactg------gtt-----------gcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTTTCCACTGCAGTAGCCAAATGGGATGCAGAGTTCTATATCAAGGTAGATG
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gtgaggatgtagtcagtattcttcaataactagtgaattcaactatacttttctggcactagccctgacatatttactgtgcgttgtttattgaacaacgcagGACCATGTTGAGGGATATCATGAACTCTCAGCTAAGACAAAAATATTCTTCTCTACTGCTGTTGGCATCTGGGACGCTGACTTCTACGTCAAGGTCGATGMapped 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|116483091|gb|EG525683.1|EG525683EST: ATAGAGCTATTGATTCAGAAGATGCTCAACACAAAGACTTCCTTAGGCTG GAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTT
genomic: ATAGAGCTATTGATTCAGAAGATGCTCAACACAAAGACTTCCTTAGGCTGgtgagacgat ... ctggttgcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaggatacagtttttcacttttcttcctgtttaaaattcttactggttgcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTTTCCACTGCAGTAGCCAAATGGGATGCAGAGTTCTATATCAAGGTAGATG
ttcttac putative branch site (score: 2)
ttcttact CT-rich tract
tgtttaaaattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagacgattctatatttctatgaaaggatacagtttttcacttttcttcctgtttaaaattcttactggttgcagGAGCATGTTGAAGGATATCACGAACTCTCAGCAAAAACCAAGATATTCTTTTCCACTGCAGTAGCCAAATGGGATGCAGAGTTCTATATCAAGGTAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG