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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag

Basic information

species Zea mays
transcript GRMZM2G010044_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g03260.2 (Oryza sativa), 5'ss of exon 9
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctact-tggcttacttgaaacttttttt--cttaatccag-
||| ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||| || ||||| ||| |||||||||| |||||||||||||| |||||||||  | ||||||   |  |||  |    || | | | |    || | |  | |    |   |||| ||   ||||    |  ||||    |||||      
AGAGTGCAAAGATGTCAAGATTGACCGGGTCTATATCGGTTCTTGTACTGGAGGTAAAACTGAGGACTTCTTTGCTGCTGCGAAGGTGTTCTTAGCTTCGgtaagaggcttgaatc---ttgtggcttggtgacatatgaccca--agtcattttgtttatttagtactatgagatactcattatgttttagaacttaagaggag

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag-----
|||||||||||| ||||| || ||| |||| || || |||||||| |||||||| ||||| ||||||||  | ||||| || ||  | |||   ||  | |||||  | |    ||  |||    | |  ||||   ||||  || ||  ||  | | |      |    |    |  |  ||   |   ||||     ||     
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaag--ttccacttcttgtctgtatcttagtac---tcatgctt-agctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 12
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag--
|||||||||||| ||||| || ||| | || |||||||| ||||| |||||||| || || |||||||| || ||||| || || || ||    || || |||||  |    |      | |   | |  |       | | || |     || ||          | |    || ||||      | | ||| | | ||   
AGAATGCAAAGACGTGAAAATTGACAGGGTGTATATTGGATCTTGTACTGGTGGAAAAACTGAGGATTTTCTAGCTGCAGCCAAAGTTTTTCATGCTTCAgtaagtttttctagcttacttagcttcttcgaggacaacttgttacttcgttcttaatttgcattcattg---tttcttgttgtggtatatctaatttcacat

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 12
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag---
|||||||||||||||||| || ||| | || |||||||| |||||||||||||| || || |||||||| || ||||| || || || ||    || || |||||  |  |  |||   || || | | | ||     |||   |   | ||  | |        | | |  | |   ||    | | | ||| | | ||    
AGAATGCAAAGATGTGAAAATTGACAGGGTATATATTGGATCTTGCACTGGTGGAAAAACTGAGGATTTTCTAGCTGCAGCCAAAGTTTTTCATGCTTCCgtaagt-ttttctatcttctcttgctct-tctagg-accattgattgtaactt-tgttgttaatttgcatatcgtgtctgttgttgtgtgtctaatttcacatc

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 11
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaag---aatcctgaatcaggtcatggtgtatgtacc---tgtcatctttcag--acctcctatcccatggctacttggcttacttga-aactttttttcttaatccag
||| ||||| ||||| ||||| ||||| || || ||||| || ||||||||||| ||||| || |||||||||||||||||| || |  |   |  ||| || ||       ||  ||  |    |||| | | | |    ||| || |||  |    | | | |   ||   |   |     |  ||  ||   |  || |||   |||
AGAGTGCAAGGATGTTAAGATTGACCGCGTTTACATTGGGTCATGCACTGGTGGAAAGACTGAAGATTTCCTTGCTGCTGCAGAGCTTCTGGCAATCTCAgtgagtccggaactttattcgaaattggtttttttgctctatgtaatgtttatgcagtcactttttatataattgagtaatggaagtgctaatactcgtttttatgacag

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ16666 (Selaginella moellendorffii), 5'ss of exon 11
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcag-gtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag
 || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| || || ||  | ||||| || ||| |        ||||   || |  | ||| | |  |      | ||| ||||| ||  | | | |    | | |||| |   |  ||  ||| |                        
GGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAAGACTTTGTAGCTGCAGCCAAGCT--------CCTCAACAA-AGCCgtgagtaaaagatcctttttatctacct-tcgccctgcggcttacatttcccttctttgtttaacttccgcag--------------------

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ32611 (Selaginella moellendorffii), 5'ss of exon 10
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag
 || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| ||||| ||  | ||||| || ||| |        ||||   || |  | ||| | |      | | | | |   |  |  | | | |    | | |||  |   |  ||  ||| |                        
GGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACTTTGTAGCTGCAGCCAAGCT--------CCTCAACAA-AGCCgtgagtaaaa--gagctttttttttttagctccctgcggcttacatttcctttctttgtttaacttccgcag--------------------

upper sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ16664 (Selaginella moellendorffii), 5'ss of exon 6
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag
  | |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| |||||  |  | | ||| || ||| |        ||||   || |  | ||| | |        | | |    |  ||  | | | |    | | |||| |   |  ||  ||| |                        
GAACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACGTTGTAGTTGCAGCCAAGCT--------CCTCAACAA-AGCCgtgagtaaaagagcttttttttctaccttcgccctgcggcttacatttcccttctttgtttaacttccgcag--------------------

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|7162228|gb|AW519835.1|AW519835
EST:     GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG
genomic: GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG
EST: gi|91051661|gb|EB162079.1|EB162079
EST:     GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTTTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACCCAAAAG
genomic: GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG
EST: gi|7137997|gb|AW499377.1|AW499377
EST:     GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCG                         GGAAAGAAGGTTAAAGTTCCCCCATTTCTTGTCCCTGCCACACAAAAG
genomic: GTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG

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), 48 (downstream exon)
Score: 30

AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 117

AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG


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

AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 43

AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcc ... cttaatccagGGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG