Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttttgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 10
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttt-tgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
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--------------------------------------------tgtagtgtgataagtaataaccatattatttgt---ttctttatttttgggaa--------------tatgaatttatatctgcaaataat--aatggtaattttccttg---attttc--------tagGTTTGTATTTGATGCCATGCATGCTGTGACTGGTGCATATGCGGATCCTATTTTTGTTGAGAAACTTGGAGCTGATCCG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 10
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttttgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
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---------------------------------------------------------gggctatctca--actcaagggtcatggctggttataatgt---ttaaggttctatgaga-------atcccacaatct--ttaaatttattgc-atttttttttattgt-tttagGTTTATATTTGATGCCATGCATGCAGTTACTGGTGCTTATGCTAAACCCATCTTGGTTGATAAACTCGGTGCTAGTCTG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 10
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttttgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
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--------------------------------------------------------agggctatccca--actcaagggtcatggctagttataa---catttaaggttctatgagaatcccacagtctctaaatttactgtatttttt-----ttattatg-------tcagGTTTATATTTGATGCCATGCATGCAGTTACTGGTGCTTATGCTAAACCCATCTTCGTTGATAAACTCGGTGCTAGTCTG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttttgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
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------------------------------------------------------------ttttcttcctataggaa-----tgattaaatcttgaagtattggacatggttgaaagtta---tattccatgattcagggttatttcatgt--ttcattttactt---ttcagGTTTACGTTTGATGCCATGCATGCAGTTACAGGCGCCTATGCAAAACCCATCTTTGTGGACAAGCTAGGAGCCAGTCCAMapped 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|125255971|gb|EL270056.1|EL270056EST: GTTTTCGACTTTGATCTCATCAGAGGTCTTCTTTCAAGATCAGATTTTGG GTTCATGTTTGA
genomic: GTTTTCGACTTTGATCTCATCAGAGGTCTTCTTTCAAGATCAGATTTTGGgtatgttctt ... ttgcctttagGTTCATGTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
atttgat putative branch site (score: 5)
ttttttgttgttcatt putative PPT
tatgatttgatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcttacatctagagccaaataggctagaagcttttgtcttttttggggttttgatggtcctattatttgcgccttctgtctggttgcagagtcgctcaacatgctaagaaccgaaactagcctatgatttgatgatattttttgttgttcattttccttgcctttagGTTCATGTTTGATGCCATGCATGCTGTTACTGGTGCTTATGCGAAACCAATTTTTGTCGACAATCTTGGAGCCAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG