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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttcttcaatcattatatgctctaatttggagtaaagcttgctatgacttagttgaatgctattttagggttcaattggattggaatggtatctta...

Basic information

species Zea mays
transcript GRMZM2G015902_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015902_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g25720.1 (Oryza sativa), 5'ss of exon 4
GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttcttcaatcatt--atatgctctaatttggagtaaa---gcttgctatgacttagttgaatgctattttagggttcaattggattggaatggtatctta
|| | |||||||||||| || |||||||| || || ||||| ||||||||||||||||||||||||||||||||||  ||||||    |  |   | || |||  |||  |  |       ||| |     ||| |  || | | ||   |   ||      |||    ||  ||    
GTTAGGAAGAAGAACTCGGAAGAGAGCTCAACGCAGTGGACCACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtaagttcttgtgccccttcgtttgttcttgtttataaaaggttcatttgttcatgttta-taaaaggttgttaaggtagtcttccatattatgttgtaat----

upper sequence: GRMZM2G015902_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S41_135V6.1 (Physcomitrella patens), 5'ss of exon 4
GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttcttcaatcattatatgctctaatttggagtaaa--gcttgctatgacttagttgaat--gctattttagggttcaattggattggaatggtatctta----------
|||   || | |||   |||||||||||| ||||||||||||||||| ||||||||||| || || ||| | ||||  ||| ||    |||| |        | |  |  | |    | ||||||   | | ||  |   |||  |||  |  ||      |    |    |  |             
GTACGAAAAAGGAATGGAGAGGAGAGCTCCACACAATGGACAACTGGAATTGCTGAAGTACAACTACCTGTAGAgtaagttatttttacatttttaaggtggaataagcttcatttacatgctatagatcatttccactagcttgtttgagactcctacaaaaaacaccaatgccgctcttggtacag

upper sequence: GRMZM2G015902_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S14_49V6.1 (Physcomitrella patens), 5'ss of exon 4
GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgtt-cttcaatcattatatgctctaatttg--gagtaaagcttgctatgacttagttg--aatgctattttagggttcaattggattggaatggtatctta-----------------
||    |  |  ||  | ||||| ||||| ||||||||||||||||| ||||| ||||| ||||||||||| ||||| | | |||  |  ||| | || |  ||   |   ||| |    |  ||   |  |  |   | | ||| ||  |  ||     |   || ||      || |                 
GTGCGAAGAAGAAATGCTGAGGAAAGCTCCACACAATGGACAACTGGTATTGCCGAAGTGCAGCTGCCTATAGAgtgagctactttgacaattttgtgatggaaaaagttaagttatatgttttagatcagaactagtacttctacttgtgtatttgcgagtcctgtaacaacccctaatgctgcactttgtacag

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|91048276|gb|EB158694.1|EB158694
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|76935876|gb|DV174501.1|DV174501
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|149014683|gb|EE044352.2|EE044352
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|211001836|gb|FL114782.1|FL114782
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|211001838|gb|FL114784.1|FL114784
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|71332986|gb|DR803518.1|DR803518
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|76018908|gb|DT946078.1|DT946078
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|20802771|gb|BQ293821.1|BQ293821
EST:     AGCTCGACACAA-GGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|211001837|gb|FL114783.1|FL114783
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|211001833|gb|FL114779.1|FL114779
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|78116755|gb|DV535142.1|DV535142
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|91870478|gb|EB400898.1|EB400898
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|148960852|gb|EE011528.2|EE011528
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|71446263|gb|DR827313.1|DR827313
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|71437898|gb|DR818948.1|DR818948
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGATACCGAGGCGGCTAATAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|211469331|gb|FL299250.1|FL299250
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCG
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCG
EST: gi|71770078|gb|DR968015.1|DR968015
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
EST: gi|71323571|gb|DR798454.1|DR798454
EST:     AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGA                         GTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA
genomic: AGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCA

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), 43 (downstream exon)
Score: 19

GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCAAGAGAAAAGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 25

GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCAAGAGAAAAGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 32

GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCAAGAGAAAAGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCA


Block sizes: 39 (upstream exon), 29 (downstream exon)
Score: 11

GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttctt ... atctccacagGTACAAATTAAGAAACATCGAAGAAACCGAGGCGGCTAAAAAGTTGCTGCAAGAGAAAAGGCTTGCAAGAAAACCAAAACCAGATGCAAACATTCCATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAGAAGAAGAACTCAGAGGAGAGCTCGACACAATGGACAACTGGCATTGCTGAAGTTCAGCTGCCTATTGAgtgcgttcttcaatcattatatgctctaatttggagtaaagcttgctatgacttagttgaatgctattttagggttcaattggattggaatggtatctta

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC