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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcag

Basic information

species Zea mays
transcript GRMZM2G075719_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac---tactactgca--tccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcat---gtgttgttttctttgcag
|||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| |||||| ||  |   |  | |||||  |||  |    |||    | || | |  |||  | | |  |  | |||||||||   || || |||| | |||||
GCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTGgtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcatt--atcttatgcattttgtatttttttttctgcag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagc--ctgtatggccc-cattgtgatctacggaccgtt--gaccttatgcatgtgttgttttctttgcag-----
|||||||||||||||||||| || ||||| || ||||| ||||||||| |||||||  |||| ||  | ||||| |  ||      | |||||   |||     ||||       |   || ||     |       |   ||| | | |  |||       |         
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgta-agatatgggaccagcatctcatagtaatagtataaattataaaatggtcaggaaatgaaaagggttttaggaaaggattggaagaagtaggatcatg

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgac------cttatgcatgtgttgttttctttgcag------
|||||||||||||||||||| || ||||| || ||||| || |||||| |||||||  |||| ||  | ||||| |  |||     |  ||||   |||  |  || || |    |  ||  | || |  || |        |     | ||      |  |  |  |      
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGAACTGTTCGACTGCAGTTGTGgta-agatacaggaccaacatctcatagtataaattgctcag--gaaatgaaagggcttttaagaaaggattggaagaagtaggaaatcatgggtgggatagt

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattacta--ctactgcatccgttagc--ctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttcttt--gcag
|| ||||||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | |||||  ||    |  ||  | ||    |      ||| |      |||||      |      | |||       |  | |  |   || |    |||
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataatt---actactactgc-----atccgttagcctgtatggc-cccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcag-
||||| |||||||| ||||| || |||||||| ||||||||||||||| | || ||  |  | ||||||||||   |||     |  |  |||     | | ||| |  | ||| || ||||     || |      |  |  | ||    |  | || | || | || || 
GCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagattttagttcttgatgctttagacctgtttgtatatattgctcccacaaatatatttttgtctctcccatttcaaaaatatt-tattttctgaagt

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 2
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtgatcta-cggaccgttgaccttatgcatgtgttgttttctttgcag---------
||||||||||||||||||||||| |||||||| ||||| ||||||||| |||| ||  | || ||  | ||||| |  | |  | |||  ||   |||      ||  |  ||    | | |   | ||  |||    | | |   | |  |||| |||             
GCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTGgtaaagatccagcaacta-ataatttattgcaaatatctacagatgggtgtggtgaacttttgtttcttttcccttctccttttttttttttttttttttg

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 3
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtg---ttgttttctttgcag
|| || || |||||||| |||||||||||||| ||||||||||| ||  | |||||| | || || |||||||  |     | |||||| | | |   ||   |||     | | |         |  |   |  || | |  |||      | |   | |||||
GCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTGgtg-agcacttgctactgga-cagccggcgc-tatcagtgcctcgcacgtcgttggtcagag-tctcacgtgtgttggcccgctgcgtgtgcag

upper sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtg-atctacggaccgtt----gaccttatgcatgtgttgttttctttgcag----------
|| || ||||| |||||||| || ||||| |||||||||||||||||  | || ||| | || || || ||||| | || |||       |  | |||     | | ||  |||| || |  | ||   ||||     || ||   | | |     | |   | ||           
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgta-actttcta-----agaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg

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|32836609|gb|CD976287.1|CD976287
EST:     GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|211109341|gb|FL282964.1|FL282964
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|32840351|gb|CD980032.1|CD980032
EST:     TACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: TACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|32839843|gb|CD979524.1|CD979524
EST:     TACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: TACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACT-CAACTCTG                         GGATACAGCTGGTCGGGAAAKGGTTCAGGAGTTTAATTCCAAGCTATATCA
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAA-GGTTCAGGAGTTTAATTCCAAGCTATATCA
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG

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: 49 (upstream exon), 47 (downstream exon)
Score: 398

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 340

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 686

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcag

- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGA