Sequence
atgc intronic sequence ATGC exonic sequencegtacgctctatttccatactaagcttaacgtaagcaacttaacatggtttattcataagaaaagtttttatctttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57410.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 10
---gtacgctctattt------ccatactaagcttaacgtaagcaacttaacatggtt---tattcataagaaaagtttttatctttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTA------CATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
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gtacttccctctatatgaagacctttattctgcgatgcccctccctctaaagcaggttccttgtccttgattatgagatttgtgagtgtactgattacagGTGGATATGCGTGATTTCTTAAATGCTCCTAATGGACTACCAAAGCAATCTCTCACTGGCAATGAAAGAGTTGAAAGTGATCCTTCACAATCTCCATTGG------
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 10
---gtacgctctattt------ccatactaagcttaacgtaagcaacttaacatggtttattcataagaaaagtt---tttatctttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTA------CATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
| | |||||| | | || | || | | || || |||| || | | | || || | || ||| |||||||||||||||||||||||||| ||||| | | | | || |||| | ||| | | ||| ||||||||||||||||||| |||
gtacttccctctatatgaagacctttattctgcgatgcccctcccgctaaagcaggttccttgacctagattatgagattcgcgagtgtactgattacagGTGGATATGCGTGATTTCTTAAATGCTCCTAATGGACTACCAAAGCAATCTTTCACTGGCAATGAAAGAGTTGAAAGTGATCCTTCACAATCTCCATTGG------
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 10
gtacgctctatttccatactaa----gcttaacgtaagcaact--taacatggtttat-tcataagaaa----agtttttatc--tttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTA------CATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
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-tatttttcttatcattagtaatggaaattgttctaaggagctgtcatctttgtttatgtggtaacaggttctaacttctacaggtatgattgacttgcagGTAGATATGCGTGATTTCTTGAATGCTCCAAATGGGTTGTCCAAGCAATCTTTGGTTGTCAATGAAAGATTTGATACAGATGCCTCACAGTCCCCATTGG------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|86047423|gb|DR343178.1|DR343178EST: AATTGATGGCTGAGAACACTAGTCTAAGAGCATTACTTCGATCCATGCAG ACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCT
genomic: AATTGATGGCTGAGAACACTAGTCTAAGAGCATTACTTCGATCCATGCAGgtacgctcta ... tttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCT
EST:
gi|86047424|gb|DR343179.1|DR343179EST: AATTGATGGCTGAGAACACTAGTCTAAGAGCATTACTTCGATCCATGCAG ACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCT
genomic: AATTGATGGCTGAGAACACTAGTCTAAGAGCATTACTTCGATCCATGCAGgtacgctcta ... tttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaacttaacatggtttattcataagaaaagtttttatctttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
acttaac putative branch site (score: 3)
ttttgtt putative PPT
tttattcataagaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgctctatttccatactaagcttaacgtaagcaacttaacatggtttattcataagaaaagtttttatctttggttttgttgcagACAGATATGCGTGATTTCTTAAATGCTCCAAATGGGTCAGCTACATTGGCTGGAAGTGAGAAACGTGAGGCTGATCCTTCACAATCTCCACTGGGTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT