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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccattgtgctgtgaagtttcactgctgatcttttgcagtcagttcatcagataaacacatctcggctttacttgatctttttttgctcttccgtttttttattttaactgattattcatggattgaatgctgaacag

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 11
GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccattgtgctgtgaagtttcactgctgatcttttgcagtcagttcatcagataaacacatctcggctttacttgatctttttttgctcttccgtttttttattttaactgattattcatggattgaatgctgaacag
||||| ||| || |||||||||||||| ||  | || ||| ||||| |||| ||||| || ||||| ||||||||||| ||||||||||| ||||||||||||||   || || ||      |  | |||| ||           ||||| ||   ||  |||    ||   |||   |  | ||     |  || | || ||| | || | |    |  ||      ||||||| |  ||||
GAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat-gtact------tcacgctgccgaca---------cagttgatattattgaca----tcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggtt------ttgaatgtttgacag
















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|60338877|gb|DN205850.1|DN205850
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|71764040|gb|DR961977.1|DR961977
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|7227784|gb|AW566425.1|AW566425
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|32860149|gb|CD999830.1|CD999830
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|148931219|gb|EC873988.2|EC873988
EST:     AAGAAACTTTCTCCAGACCAATTAGCAGCTTGCTG                         AAAGCCCAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: AAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|32860148|gb|CD999829.1|CD999829
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60400196|gb|DN233003.1|DN233003
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|148966756|gb|EE017836.2|EE017836
EST:     TTTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCCCAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|148958743|gb|EC905020.2|EC905020
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|32934959|gb|CF039771.1|CF039771
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|32931620|gb|CF036432.1|CF036432
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60344484|gb|DN211457.1|DN211457
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA

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), 46 (downstream exon)
Score: 129

GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 81

GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 53

GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccat ... tgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaaggccattgtgctgtgaagtttcactgctgatcttttgcagtcagttcatcagataaacacatctcggctttacttgatctttttttgctcttccgtttttttattttaactgattattcatggattgaatgctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT