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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatctcgtatcgtgtgtcgctcttcacatctgatataatttgttaaccaacgcaagcagggttgactcaataattcatattttgtaaattaagttatttacatgattccatatgttgttctgacttctgagtatacaaataaactttag

Basic information

species Zea mays
transcript GRMZM2G066578_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066578_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g33250.2 (Oryza sativa), 5'ss of exon 4
TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatctcgtatcgtgtgtcgctcttcacatctgatataatttgttaaccaacgcaagcagggttgactcaataattcatattttgtaaattaagttatttacatgattccatatgttgttctgacttctgagtatacaaataaactttag
| || ||||||||||||||||| ||||||||||| || ||||| ||||  |||||||||| ||||||||||||||||||||||||||||||||| || |||||||||  ||  |||  |           || ||     |  ||   |     ||||       |||||||   | |  ||| |||      |    ||||| | |                                               
TTGATTTCATGAACAACATGGGGCACTGCAACTTCGAGTTGGTACCCAGCTGGCTCTTCACATGGTTCCCTCCTCTCAAGTATCTCATGTACACGCCATCgtaagtacttc--atcaggctcttaataatacttccttcttccttaaatgtttgacgcc------gttgacttttttaaacatgtttgaccgttcgtcttattcaaaa----------------------------------------------
















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|78076046|gb|DV504480.1|DV504480
EST:     GGCTCTTCAAATGGTTCCCTCCCTCTCA-GTATCTCATGTACACACCCTC                         GTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGGTCAT
genomic: GGCTCTTCAAATGGTTCCCTCC-TCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCAT
EST: gi|149101383|gb|EE187500.2|EE187500
EST:     GGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCCTC                         GTTTCATTCTCTTCCCCACACTCAGTTCAGGGACAA-CTACTCCCTGT
genomic: GGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCC-TCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGG-ACAAACTACTCCCTGT
EST: gi|148956804|gb|EC902698.2|EC902698
EST:     TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTC                         GTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTA
genomic: TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTA
EST: gi|76018388|gb|DT945558.1|DT945558
EST:     TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTC                         GTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCAT
genomic: TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCAT
EST: gi|148999701|gb|EE036698.2|EE036698
EST:     TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTC                         GTTTCATTCTCTTTC-CCACACTCAGTTCAGGACAAACTACTCCCTG
genomic: TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTT-CACCACACTCAGTTCAGGACAAACTACTCCCTG
EST: gi|78091933|gb|DV520307.1|DV520307
EST:     TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTC                         GTTTCATTCTCTTCACCACCCTCAGTTCAGGACAAACTACT
genomic: TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACT
EST: gi|93015094|gb|EB640614.1|EB640614
EST:     TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTC                         GTTTCATTCTCTTCACCACACTCAGTTCAGGACAAA
genomic: TGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAA

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 114

TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCATGCCATTCTATGACTACATATATAACACCATGGACAAGTCATCGGACACG


Block sizes: 34 (upstream exon), 19 (downstream exon)
Score: 4

TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCATGCCATTCTATGACTACATATATAACACCATGGACAAGTCATCGGACACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3684

TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatct ... taaactttagGTTTCATTCTCTTCACCACACTCAGTTCAGGACAAACTACTCCCTGTTCATGCCATTCTATGACTACATATATAACACCATGGACAAGTCATCGGACACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGACTTCATGAACAACATGGGCCACTGCAACTTTGAATTGGTGCCCAATTGGCTCTTCAAATGGTTCCCTCCTCTCAAGTATCTCATGTACACACCCTCgtaagtatctcgtatcgtgtgtcgctcttcacatctgatataatttgttaaccaacgcaagcagggttgactcaataattcatattttgtaaattaagttatttacatgattccatatgttgttctgacttctgagtatacaaataaactttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC