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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacaatctgatttttagctttttgactgcacgtattagccagtgtatattccatccaagtcacatatttttaatattttaataaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG

Basic information

species Zea mays
transcript GRMZM2G180863_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 3'ss of exon 6
gttcacaatctgatttttagctttttgactgcacgtattagccagtgtatattccatccaagtcacatatttttaatattttaataaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG
|||  ||   |  ||  ||    |  || |   | ||||    ||||             | | |  |  ||||  | |||||||| |  ||||| ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||| ||||||||| | ||||||||||| |||||
gttagcatctt--ttcataatggtaagattctgcatattttgtagtgcgctcgttcaattattaatctcatttttttcttttaatacatcccagGAACAATTACTAGTGCAGCTGCTTTGTTAAAACAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAG

upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g41360.4 (Oryza sativa), 3'ss of exon 6
gttcacaatctgatttttagctttttgactgcacgtattagccagtgtatattccatccaagtcacatatttttaatattttaataaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG------------------
|||  ||   |  ||  ||    |  || |   | ||||    ||||             | | |  |  ||||  | |||||||| |  ||||| ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||| ||||||||| | ||||||||||| |||||                  
gttagcatctt--ttcataatggtaagattctgcatattttgtagtgcgctcgttcaattattaatctcatttttttcttttaatacatcccagGAACAATTACTAGTGCAGCTGCTTTGTTAAAACAGGAGGGAGCAGAGGCTGTCTATGCTTGTAGCACACATGCTGTCTTCAGGTTTGGCAGTTGGTTTAT
















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|60341300|gb|DN208273.1|DN208273
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|71770133|gb|DR968070.1|DR968070
EST:     CGTGAAAGAAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|211094604|gb|FL027759.1|FL027759
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCSS-G-CTTTTGTTAAAGCAGGAGGGAGCAGAAGCT
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTT-GTTAAAGCAGGAGGGAGCAGAAGCT
EST: gi|149006975|gb|EE040194.2|EE040194
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|50325134|gb|CO520260.1|CO520260
EST:     ATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: ATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|60358780|gb|DN225753.1|DN225753
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|148947743|gb|EC893226.2|EC893226
EST:     ATTGATGACATGATTGATTCAGCAG                         GGACAATCCCTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: ATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|149088667|gb|EE177785.2|EE177785
EST:     AAAGGAAAAGTGGCTATCTTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: AAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|6626351|gb|AW257883.1|AW257883
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|211094605|gb|FL027760.1|FL027760
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTA--GC-GCSSCTTTGTTAAAGCAGGAGGGAGCAGAAGCT-
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|24769265|gb|CA404394.1|CA404394
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|31354391|gb|CD438748.1|CD438748
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|50339734|gb|CO534860.1|CO534860
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
EST: gi|50322471|gb|CO517597.1|CO517597
EST:     CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG                         GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG
genomic: CGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTG

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: 223

GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 444

GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAGgttcacaatc ... taaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccagtgtatattccatccaagtcacatatttttaatattttaataaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG
                                       ttttaat  putative branch site (score: 203)
                atccaagtcacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacaatctgatttttagctttttgactgcacgtattagccagtgtatattccatccaagtcacatatttttaatattttaataaaatccagGGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT