Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gtgagtcttcaaattcttttggc-atcat-tttaacagtccattgcctaagcgctttgcattatctggat-----atatattatttgtt-acagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
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gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 3
-----gtgagtcttcaaattcttttggcatcattttaacag---tccat-tgcct--aagcgctttgcatt--atctggatatatattatt-tgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
|| || | || | || | | | || || |||| | | |||| || ||| | || | |||||| || | || ||||||| ||||||| || ||||||||| || || | || | ||||| ||||||||||||||||| ||||| || |||||
taatggtttgtatgataacacaaatgtgaaaagtagaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 4
gtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
|| ||| | || | | | ||| || |||| || | || || | | ||| | | ||||| | | ||| ||||||||||| |||||||| ||| |||| || || || || ||||| ||||||||||| || ||||||||||||||
gtaagtaataaacctgatataatttcagtt-gtcagtttatggt---agttagctgtaaca-ctgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 4
gtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
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gtaagtaataaacctgatataatttcagtt-gtcagtttatggt---agttagctgtaaca-ctgaccagagattatgttatgcagGGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
|||| |||| || | | | |||| ||| | || ||| | ||| | ||| ||||| ||| | |||| ||||||||||||||||||||| |||||| | || || |||||||||||||||||||||||||| || ||||||||||| ||
gtgaatcttaaa---cctgttgcat--tttcagttttcttttgtatgg-----ttgtaatat-tggatgggcattctctgtttcagAGATAGAGCTGGTGGATATACAAGATTACTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAMapped 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|86077821|gb|DR373578.1|DR373578EST: GGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA AGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGG
genomic: GGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAAgtgagtcttc ... tttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGG
EST:
gi|19875182|gb|AU236013.1|AU236013EST: GGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA AGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGG
genomic: GGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAAgtgagtcttc ... tttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
ttttaac putative branch site (score: 2)
attatctggatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT