Sequence
atgc intronic sequence ATGC exonic sequencegttagttaagtcttgtatttaatatgtcaataataaactacatttctcctgagagaattcctaatattggtcaatttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48850.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------------------------gttagttaagtcttgtatttaatatgtcaataataaac--tacatttctcctgagagaattcctaatattggtcaatttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
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gttttatcctagtcccctgttgttttacagttatattatttattgttttcgctacatctagctgcattctagattaaaaaaat-actagtaaatagtataacaccgttgtcttagtatttataatgtgtatgtccatgcagGGAGGGATATCAAATGGTGAAATTATATACTTCAAAGTAGCTTTCAAGCCAACCGCGACTATTGGG----
upper sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 10
------------------gttagttaagtcttgtatttaatatgtcaataataaactacatttctcctgagagaattcctaatattggtca-atttgta--tagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
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gtatttgtgctgttctataattactaattagttttttctagatatgcactgacagtcacatttcta-tatttgttttacttatattatctgtattgacaatcagGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA----
upper sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G35560.2 (Glycine max), 3'ss of exon 10
--------------------------gttagttaagtcttg-tatttaatatgtcaataata-aactacatttctcctgagagaattcctaatattggtcaatttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
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gtatttgtgctgttctgtaattactaattagttgtttctagatatgcactatatcagtcacatgtctatatttgttttacttatattatctgtattga-caatc-----agGGTGGAATTTCCAATGGGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA----
upper sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 10
------gttagttaagtcttgtattta-atatgtcaataataaactacatt--------tctcctgagag-----aattcctaatattggtcaatttgt---atagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
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gtacttgttatgtactttaagcatttgtatgtgtttgggattagatttgttatgcaccattttttaagcatcttcagtccttgagatcgtttctgctgacaaacagGGCGGAATATCAAACGGGGAAATCATAAACATAAGAATAGGTTTCAAGCCAACATCTACAATTGGA----Mapped 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|124939076|gb|EL015649.1|EL015649EST: TGAAAATGGAAGAATACGTACCAGAACCAACCGATCTGGTAGGAATTCAG GGAGGGATCTCAAATGGTGAGATAATAAACA
genomic: TGAAAATGGAAGAATACGTACCAGAACCAACCGATCTGGT-GGAATTCAGgttagttaag ... atttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataataaactacatttctcctgagagaattcctaatattggtcaatttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
tcctaat putative branch site (score: 2)
aatttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttaagtcttgtatttaatatgtcaataataaactacatttctcctgagagaattcctaatattggtcaatttgtatagGGAGGGATCTCAAATGGTGAAATAATAAACATGAGAGTAGCCTTCAAGCCAACATCAACAATTGGAGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG