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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggctacatatgctgttattataccgtgcatgacgtgagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG

Basic information

species Zea mays
transcript GRMZM5G845755_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 6
-gttggctacatatgctgttattataccgtgcatgacgt-gagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG
 |    || | |  |      |  ||  |  | |||  | || |     || |||   |  |    | | ||||  ||    ||   ||| |  |||  ||||||||||| |||||  | ||||||   || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||
tgagtactgcttcagtaaaagtcttattgaacttgagctagatatgtgataaatcatctttagttatttgtgttgtttcc--ctgactccctgcattcacagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
















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|5846756|gb|AI999839.1|AI999839
EST:     CCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     CCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|31359089|gb|CD443446.1|CD443446
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|60345260|gb|DN212233.1|DN212233
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     TGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: TGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     CANNNNNNNACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     ACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG
genomic: ACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAG

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), 49 (downstream exon)
Score: 263

ATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

ATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

ATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 168

ATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttgacattc ... ttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG
                                        tccattt  CT-rich tract
     atctattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctacatatgctgttattataccgtgcatgacgtgagaccatttagatctattaaatgcctctctgttagttattgctacatccatttattatcagGTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - gctacat
- - - - - - tgctgtt
- - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacatc