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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaatttgttatgtaata...

Basic information

species Zea mays
transcript GRMZM2G068255_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgta---aacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaatttgttatgtaata
  | ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| || |||||||||||||||||||||   ||  |        ||  |   |   |   |        ||    ||| | | | |      ||  |||  |  ||  ||||  |    |      | 
--ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggtt--ttgaaaatttacctgaggtagccttaactgt-

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G36570.1 (Glycine max), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacgg----cccatttttatccaaaaaagcttatttgtagcaaaacttattcaacga-tccaattattgtttgccaggttctctgaaatttgttatgtaata
  | || || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| ||||| ||| ||||| | ||||  ||    | ||| |   || |       |||| | |||  |   || ||   | | |   |  ||| |||      |  || ||  ||||||        
--ATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGAgtaagtggattcctcatctaactcgagttctctttatgtttagttatgattgttgtgctagtgtgagcattttttatttcctgttcagatttttgtttga-----

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatt--tttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttc-tctgaaatttgttatgtaata-----------------------------------------------------------------------------
  | || || ||||| || || || ||||| || || ||||| |||||||||||||| || |||| ||||||||| || || ||||| ||| ||||| ||||||  ||   | |  | || |  |||    || | |||     ||    |     | | |  | |   |||  |   ||| |||  |  || || | | |                                                                               
--ATGATTATCGGCTCTTTTGCGGCGATCTTGGTAATGAAGTGAATGATGATGTTCTTTCAAAAGTATTTTCACGATTCCCTTCCTTTAACTTGGCACGGgtaagtggattactcatctagctcaaatgatttttatgtttaggaatgattgtggtgcttctgtgagcatttttctatttcctcttcagatttttgtttgaagggacagagttgttaatatttgtgtatcttaacgtaggtcttgcttaatgacctgaagttatgtttgatcttgtctag

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacgg---cccatttttatccaaaaaagcttatttgtagcaaaacttattcaacga-tccaattattgtttgccaggttctctgaaatttgttatgtaata
  | || || ||||| |||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||| ||||| ||||| ||||||||| | ||||  ||   | ||| |   || ||       ||| | |||  |   || |    | | |   |  ||| |||      |  || ||  |||||| || |   
--ATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggttctcatctaactcgaattctctatatgtttagttatgattgtcgtgctagtgtgagcattttttatttcctgttcagatttttgtt-tgaa---

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaa--tttgttatgtaata------
  | ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||| |  | || ||  ||||||| ||||| | ||||| | |   || | | |||       ||| |  |    |    |||||||   |||   ||     |   ||  |  |    ||  || || |||| ||       
--ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaa-ctgtgtatatctctcctc-----cttttcggctttagtgattattcat--atctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaa----aagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaatttgttatgtaata---
  | || || ||  | || ||||| ||||| ||||| || || || ||||||||||| || |||||||||||||| ||||| |||||||| ||||| || ||||   |   || |||  |  ||     |  ||| ||| ||  |  |   | || |  ||   || |||||||||  |||    ||   ||| ||   ||      
--ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGAgtaa---gtttatatttccctcaagttttatacttttttttattagga---actctaatattagat-attgtttgcttggtgtattgttgttttttgcatatcctct

upper sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 3
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaaa----agcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctg-aaatttgttatgtaata-
  | || || ||  | || ||||| ||||| ||||| || || |||||||||||||| || |||||||||||||| ||||| |||||||| ||||| |  ||||      |  ||| || |||       | ||| | | ||  |  |   |||| |  ||   || ||  |||||  ||| |   |  |  || ||    | |  
--ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAAgtaagt--ttctatttcattcaagttctttaccttttctttattagga---attctattattagat-atcatttgcttggtgcatggtgagctttttgcccattct

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|89248698|gb|DY620484.1|DY620484
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|211002219|gb|FL464441.1|FL464441
EST:     TTCCATCGTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGTACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: TTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|71320385|gb|DR796941.1|DR796941
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|31612073|gb|CD568695.1|CD568695
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|74235772|gb|DT643686.1|DT643686
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|78083193|gb|DV511586.1|DV511586
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|78080540|gb|DV508952.1|DV508952
EST:     ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: ATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
EST: gi|60397448|gb|DN230264.1|DN230264
EST:     CTCTCCAAAGCATTTTCACGGTTTCCATCCTTTAACATGGCAAGG                         GTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC
genomic: CTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcc ... tttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG