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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgcccaaaatgaaactctgtgccgcctcgtgtcatttttggtgcccagatcgatccaacttaattaatgatttccattctttaaaagaaaaaaaa...

Basic information

species Zea mays
transcript GRMZM2G042364_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042364_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g58910.1 (Oryza sativa), 5'ss of exon 2
GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgcccaaaatgaaactctgtgccgcctcgtgtcatttttg-gtgcccagatcgatccaacttaattaatgatttc-cattctttaaaagaaaaaaaa
||||||||||||||| ||||||||||| || |||||||||||||||||  ||||||||||||||||||||| |  |  ||       |     |||  ||| |||  | || ||||  |  ||  || ||  ||||  |     ||  ||| |   || |    |
GAAGGTGAGGCCCAAGATGACGTGGTCGGTGTTCCTCCAGATCTTCGTCCTGGCACTGCTCGGgttagtgcactgatcgattgatgatcatctctcccgtcttttcggtgtacccaacttaat--aatttctttaagaagagaacacgcttaagtggacattcca
















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|211124594|gb|FL137144.1|FL137144
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGAC-AGAACTTCTACTACGCCGGCCTCAAGTTCACCGGG
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGG
EST: gi|50335600|gb|CO530726.1|CO530726
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|211123823|gb|FL137137.1|FL137137
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|149099820|gb|EE185873.2|EE185873
EST:     ACATGACGTGGTCCGTCTTCCTCCAGATCTTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: ACATGACGTGGTCCGTCTTCCTCCAGATCTT-CGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|211123824|gb|FL137138.1|FL137138
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|211123825|gb|FL137139.1|FL137139
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|211123828|gb|FL137142.1|FL137142
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|78023216|gb|DV491603.1|DV491603
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
EST: gi|211124593|gb|FL137143.1|FL137143
EST:     AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG                         GCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC
genomic: AACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCC

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: 13 (upstream exon), 37 (downstream exon)
Score: 1

GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCCGACCTTCGCGTGCGCCATGAGCAACATCCTTCCTGCCATGACCTTCGTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 34

GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCCGACCTTCGCGTGCGCCATGAGCAACATCCTTCCTGCCATGACCTTCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCCGACCTTCGCGTGCGCCATGAGCAACATCCTTCCTGCCATGACCTTCGTC


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 19

GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgccc ... taccttacagGCCTGTGATAGACCAGAACTTCTACTACGCCGGCCTCAAGTTCACCGGGCCGACCTTCGCGTGCGCCATGAGCAACATCCTTCCTGCCATGACCTTCGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGGgttagtgcccaaaatgaaactctgtgccgcctcgtgtcatttttggtgcccagatcgatccaacttaattaatgatttccattctttaaaagaaaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaaa