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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaaggcaacatgcagaaaacatgtttgctagtccaactgtgtgaaacatcatattcacaaggtttcttgtgcccctctgtttttgaccatgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC

Basic information

species Zea mays
transcript GRMZM2G091503_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091503_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 5
ctttaaggca-acatgcaga-aaacatg--tttgctagtccaactgtgtgaaacatcatattca--caaggtttcttgtgcccctctgtttttgaccatgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC
   ||  | | |||||   | | || ||   |  |       ||| |    | || |  ||| |    |   | ||||||  |   || |||| ||  |  ||||| ||||||||  ||||||| ||||||||| |||| || || |||||| ||||||||||| ||||||||  ||||||||| ||||| || |||||||| |||
--ctagagtacacatgtttacatacttgaaataaccgaggtcactataatcagcaactcatttaacttaaactacttgtgtgc---tgatttt-actgttgtgtagAAACAAGCTCCGGGAATCAAGGAACGCCATATCATCTGCTGACATCACTGATGAAGTCAAGCTTGGGAACCCTGGAGAAGCATTTAATTTCAGCCAATGC
















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|32847270|gb|CD986951.1|CD986951
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|211478433|gb|FL475431.1|FL475431
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|32939995|gb|CF044814.1|CF044814
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|78111931|gb|DV530327.1|DV530327
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|26557561|gb|CA829796.1|CA829796
EST:     GTTACCGCCCCCTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATTTAGGAACGCCGTATCGTCAGCCGACATTTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|78111930|gb|DV530326.1|DV530326
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATTTAGGAACGCCGTATCGTCAGCCGACATTTTTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|193503546|gb|AM937735.1|AM937735
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAA---GCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|113702875|gb|EE680379.1|EE680379
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTTTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|20208508|gb|BQ134597.1|BQ134597
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|78544806|gb|DV622304.1|DV622304
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|60399201|gb|DN232015.1|DN232015
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|33091165|gb|CF051159.1|CF051159
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|60346742|gb|DN213715.1|DN213715
EST:     GTCACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCATCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|21809709|gb|BQ668027.1|BQ668027
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|60344808|gb|DN211781.1|DN211781
EST:     GTCACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCATCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|23357586|gb|BU645235.1|BU645235
EST:     GTTACCGCCCCCTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|60340296|gb|DN207269.1|DN207269
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|193502482|gb|AM937804.1|AM937804
EST:     GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         G---AAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
EST: gi|22520627|gb|BU079438.1|BU079438
EST:     GTTTCCGCCCCCTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATT                         GAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA
genomic: GTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGA

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: 43 (upstream exon), 48 (downstream exon)
Score: 286

TAGTGAAGAAAAAGGTCCCTGTGCTTATATTCTGCAACAAGACAGATAAAGTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 122

TAGTGAAGAAAAAGGTCCCTGTGCTTATATTCTGCAACAAGACAGATAAAGTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 91

TAGTGAAGAAAAAGGTCCCTGTGCTTATATTCTGCAACAAGACAGATAAAGTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 149

TAGTGAAGAAAAAGGTCCCTGTGCTTATATTCTGCAACAAGACAGATAAAGTTACCGCCCACTCGAAGGAATTCATCAAGAAGCAGTTGGAGAAAGAATTgtaaggacag ... catgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacatcatattcacaaggtttcttgtgcccctctgtttttgaccatgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC
                                      ttttgac  putative branch site (score: 149)
     atcatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaaggcaacatgcagaaaacatgtttgctagtccaactgtgtgaaacatcatattcacaaggtttcttgtgcccctctgtttttgaccatgttgtagGAACAAGCTTAGGGAATCTAGGAACGCCGTATCGTCAGCCGACATCTCTGATGAAGTCCAGCTTGGGGTCCCTGGAGAGGCATTCAACTTCAGCCAGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG