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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag

Basic information

species Zea mays
transcript GRMZM5G822591_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag
 || ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| || ||||| |||||| ||    | |||| |  | |   | |||   | ||  ||||| || ||||| | ||   || ||        || | |||||||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatct----tgtttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttg--cttcatgtgcag

upper sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag
 || ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| || ||||| |||||| ||    | |||| |  | |   | |||   | ||  |||||  | ||||| | ||   || ||        || |||||||||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatct----tgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttg--cttcgtgtgcag

upper sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtg-atgtttgt--ttacatatagtttactatggtaataacat--ccatcctgcgtgtgcag---------
 ||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| || || ||||| ||||||||||| || || ||||||||||| |     ||  |||| ||| |  |  |     || || |   ||  |    |   | || | |    || |  ||| |||| | |              
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaatta-gcttgcgactttcccagcctgtgggccttttttagagct

upper sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag
 ||||||||  | || |||||  | || ||||| || || |  |||||||||||||||||||| || ||| | |||||||||||||| || || || |||||||   | || ||||  ||     || |   | | |    |    |  | |||        |  |   | |||  |   |    ||
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctca--accactgttcatttttttt-catag

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|211415580|gb|FL028984.1|FL028984
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|37375445|gb|CF624160.1|CF624160
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|31664357|gb|CD573082.1|CD573082
EST:     TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|60399410|gb|DN232222.1|DN232222
EST:     TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|60395619|gb|DN228489.1|DN228489
EST:     TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|67016082|gb|CO444831.1|CO444831
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|29945571|gb|CB815707.1|CB815707
EST:     TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
EST: gi|29129934|gb|CB380638.1|CB380638
EST:     TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATCCGTGAATACNCTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC
genomic: TTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATC

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: 47 (upstream exon), 49 (downstream exon)
Score: 189

CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 349

CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaact ... gcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA