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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttggagactactactatgtgaagatatatgctctctgttcataaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG

Basic information

species Zea mays
transcript GRMZM2G425249_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 3
gttttggagactactactatgtgaagatatatgctctctgttcata--aagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgt---cacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
||||   |    |     || |||     | | || |   |  ||   |||       |   |     |  || |   |  | | ||||  |  | |    |||||||||||| ||||| |||||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||   ||||| |||| |||||
gtttcttaaggaa-----atctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG

upper sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G71697.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttggagactactactatgtgaagatatatgctctctgttcataaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
     | |  ||  |   ||   ||    ||| | ||   ||||| |||    || |  ||       |||  |||            ||||  |  ||||| ||||||||| | || ||||||||| |||| ||||||||||| ||||| || ||||||||||| ||  | || ||||||   |  |||||| | ||||
-----gtaagctttttgaat-caaaagcttataccctt--ttcatcaagaaagtgttctgt------ttttaataag----------tttttgattgcagGACTATGAGTATTCGAGTTTCAACCCAATTGCTTATGACATTGCAAACCACTTTTGTGAGATGGCTGCTAATTACCATTCAGACACTCCTCATGTTCTGG

upper sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0084g00150.t01 (Vitis vinifera), 3'ss of exon 4
gttttggagactactact--atgtgaa---gatatatgctctctgttca--taaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
        |||||  |||  || ||||   |  |  ||    |  || |   ||  ||||||   | || | | || |  |     |   |   || | | |  |||||||||||||||||||| | ||| || ||  | |||||||| || || || |||||||||||||| || ||||||||| ||  || |||||| ||  |||
-------tgactatcacttgatatgaatcaggcacttgtctgccttttagtcaatatttttggagcttaactagctgttattcatctaattctgctctctttaccagGATTATGAGTATGCAAGTTACAATCCTGTCACTTATGACATAGCAAATCACTTCTGTGAGATGGCTGCTGACTATCATACAGAAACGCCTCACATTTTGG

upper sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S50_118V6.1 (Physcomitrella patens), 3'ss of exon 4
gttttggagactactactatgtgaagata--tatgctctctgttcataaagtttttgcttcgt--accaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
      ||  | | |  | ||   || |    ||  |||||  |||  |  || || |||     |                 | | || |  | |||   |||||||| ||||| || || | |||||| || |||| |||||||||||||||||||||||||||| | || || || || ||     |||| ||| |  |  
----cagatgcaagtcatttgctgaggtggtcattttctctactcaacatcttattacttttatgattggatccctaagcttcttttttgttgtattggagcagGATTACGAGTACGCCAGTTACAACCCCGTAGCATTTGACATTGCTAACCATTTCTGTGAGATGACTGCCGATTACCACTCTGATGAGCCGCATTTGTTAA

upper sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S194_46V6.1 (Physcomitrella patens), 3'ss of exon 4
-----gttttggagactactactatgtgaagatatatgctctctgttcataaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtca-cagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
       |  |||   || |   |   | || ||  ||||     ||  | ||  || |  | | ||  |  ||| | |    |||  || ||   |||  | |||||||||||||| || || | |||||| || |||| ||| ||||| || ||||||||||| ||| | ||||| ||||||||     |||||||| |  || 
gcagatgtcaggaaggtatttgcacaagtaggtagttgct-----ttggtgaacattatattac-tattatgcttacattgttgtggtttgtcggattgggagcagGATTATGAGTACGCCAGTTACAACCCTGTGGCATTTGATATTGCCAATCATTTCTGTGAAATGACTGCAGATTATCATTCTGACGAGCCTCATTTGTTGA

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|32831253|gb|CD970931.1|CD970931
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTACGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|32831274|gb|CD970952.1|CD970952
EST:     AGTATGGCAATATCATGATTGATGATGAGACCAACGTGCTGACCATCATT                         GATTACGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTATCCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|7304609|gb|AW600548.1|AW600548
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|37422901|gb|CF649166.1|CF649166
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|71329495|gb|DR801471.1|DR801471
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|32830339|gb|CD970017.1|CD970017
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTACGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|60347369|gb|DN214342.1|DN214342
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|71321225|gb|DR797321.1|DR797321
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|89762412|gb|DY690008.1|DY690008
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
EST: gi|32830652|gb|CD970330.1|CD970330
EST:     AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATT                         GATTACGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT
genomic: AGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCAT

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: 45 (upstream exon), 46 (downstream exon)
Score: 11

CGAGTGTTCAGGTGATTACCAGTGGATTGGTTTCTGTCACAATGATCTTCAGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 129

CGAGTGTTCAGGTGATTACCAGTGGATTGGTTTCTGTCACAATGATCTTCAGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

CGAGTGTTCAGGTGATTACCAGTGGATTGGTTTCTGTCACAATGATCTTCAGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 99

CGAGTGTTCAGGTGATTACCAGTGGATTGGTTTCTGTCACAATGATCTTCAGTATGGCAATATCATGATTGATGAAGAGACCAACGTGCTGACCATCATTgtaagtgaca ... tttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG
                         tcgtaac  putative branch site (score: 99)
                                  tgtcttctctttttgt  putative PPT
                                         tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttggagactactactatgtgaagatatatgctctctgttcataaagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgtcacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - ctatgtg
- - - - - - - - - - - - - - -tatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacct