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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcctcttgcctttctctttactttgctcgtcgatttcagcgaaggttagtttgcgtgcgcggtgcgctcatagatgagtgtaatttggggaaa...

Basic information

species Zea mays
transcript GRMZM5G856436_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 2
GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcctcttgcctttct---ctttactttgctcgtcgatttcag--cgaaggttagtttgcgtgcgcggtgcgctcatagatgagtgt--aatttggggaaa
 ||||||| |||| |||||||||||||||||||||| ||||||||||||||||||||  |||| |    | | |  |||| |    ||||  |  ||   || |   |    |    || |||    ||||  ||||  |||||||     
TCCTTCCATTGCAAGCACGGGAAGGCGTACCTCTTCAATAAGGTgtaagtggcctct--ccttcccgggcctcatcttgccctcgaatttttgttcgctcgtcaaactttaggtagcgtacgccgggagatatgtgtggaatttgg-----
















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|211161884|gb|FL207305.1|FL207305
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211163480|gb|FL207315.1|FL207315
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATG
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATG
EST: gi|26558493|gb|CA830728.1|CA830728
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161885|gb|FL207306.1|FL207306
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161887|gb|FL207308.1|FL207308
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATG
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATG
EST: gi|22472703|gb|BU037183.1|BU037183
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211160285|gb|FL207293.1|FL207293
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCT
EST: gi|211161891|gb|FL207312.1|FL207312
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161881|gb|FL207302.1|FL207302
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|16927653|gb|BM080722.1|BM080722
EST:     GCCTTCCACTGCAGGCACGGAAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211160284|gb|FL207292.1|FL207292
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211458337|gb|FL363659.1|FL363659
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161888|gb|FL207309.1|FL207309
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGN                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|14243210|gb|BG840951.2|BG840951
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211163479|gb|FL207314.1|FL207314
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAATATCGCATGATGA
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGA
EST: gi|67017876|gb|CO446625.1|CO446625
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|113701952|gb|EE679456.1|EE679456
EST:     TCCAAGGCCTTCCACCGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGCCAGGAAT
genomic: TCCAAGGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|16917041|gb|BM073101.1|BM073101
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|21389991|gb|BQ528040.1|BQ528040
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|60341900|gb|DN208873.1|DN208873
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|31352331|gb|CD436688.1|CD436688
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161892|gb|FL207313.1|FL207313
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161889|gb|FL207310.1|FL207310
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|37376556|gb|CF624817.1|CF624817
EST:     TCCAAGGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: TCCAAGGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211160286|gb|FL207294.1|FL207294
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACNGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|31352347|gb|CD436704.1|CD436704
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|16925094|gb|BM078162.1|BM078162
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161880|gb|FL207301.1|FL207301
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|31351127|gb|CD435484.1|CD435484
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGATTATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161886|gb|FL207307.1|FL207307
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGAC
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGAC
EST: gi|14242748|gb|BG840532.2|BG840532
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
EST: gi|211161883|gb|FL207304.1|FL207304
EST:     GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT                         TGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT
genomic: GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAAT

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: 44 (upstream exon), 49 (downstream exon)
Score: 88

GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 59

GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 29

GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 75

GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcc ... ttatacccagTGCCAATGTGACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGTgtaagtggcctcttgcctttctctttactttgctcgtcgatttcagcgaaggttagtttgcgtgcgcggtgcgctcatagatgagtgtaatttggggaaa

- - - - CTGCAG