Sequence
atgc intronic sequence ATGC exonic sequence...agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G09810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
------agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgtt--ctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
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tatcatagcagtgcagacctgatgttcccttgacttttacatattcct-tacatgagcaaactgggactaatgctttcttcttcactcacttaat-------ttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
------agaagggtga--ttatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
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agatccatttgcttgatattataaattttctttctttgctgca--agcttgaccaacctggccaa-gacttattgttt---tcctgtcacatgtt--ttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G014610_T01 (Zea mays), 3'ss of exon 4
agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgatt--ctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
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---------------gtaccgtacgagtcgacgaacaagaattctgg--aatccgaatg--ccatccctcacctcacctcacctcaccgttttctgccgcagTTGTTCCTCGCGCTGTCGTGCTTCATCGCGATCGGGGTCAACCTGAGCCAGTTCATCTGCATCGGCCGCTTCTCCGCCGTGTCCTTCCAGGTCCTGGGCC
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
-----agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattca-ataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
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tatttgatctgcttgatgttataaattttcattcttcg---gcgcaaacttgacgaacctgg-gcatgacttactattttcttatcacatgtt--ttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCCMapped 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|164045931|gb|ES145182.1|ES145182EST: GGTTGACAGACAAACGGGTAGACATGTATGATTACAACTCTGTCTCTGTG ATGTTTATAACCCTC
genomic: GGTTGACAGACAAACGGGTAGACATGTATGATTACAACTCTGTCTCTGTGgtaagtgctc ... gattctgcagATGTTTATAACCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
caataac putative branch site (score: 2)
tttgtattcaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagggtgattatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - tatcaaa
- - - - - - - - - - - - - - - - - - -ggtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - actctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataac