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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatataataagtttgttaagcatctatgaattatgattctatttatgttattattatgttctatatttaatttaagatcacacgttaatgcttgaaccttctgcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 9
gtaaatataataagtttgttaagcatctatgaattatgattctatttatgttattattatgttct---atatttaatttaagatcacacgttaatgcttgaaccttctgcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC
                         |   |||    |  || | | ||||||| ||  || |||    || || ||| |  |   |||   |||| ||||||  | |||   || |||||||| ||||||||||| ||||||||||||||||||||||||||||| || || || |||||||||||
------------------------gtaagtgaggagtccttgt-tatatgttagtaagatattcggtgattttgaatgtgtgggaaca---taattcttgaatttcctgtctttgcagTTCCATATTCTTTTCTGTGTATTTTCTGCTGTGGCTCCTCCTGTTGTCTTCGAGGGGAAATCATTGGC
















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|76929603|gb|DV172080.1|DV172080
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTA
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTA
EST: gi|60342784|gb|DN209757.1|DN209757
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCT
EST: gi|149103005|gb|EE288366.2|EE288366
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTTTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|76018526|gb|DT945696.1|DT945696
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|29543932|gb|CB604312.1|CB604312
EST:     TGGATTGTTCTTCTTGCTTTACGTG                         TTCCCCATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: TGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|78023022|gb|DV491409.1|DV491409
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTG
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTG
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCCTGT-GTATT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCC-TGTTGTATT
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG                         TTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT
genomic: GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTT

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: 34 (upstream exon), 49 (downstream exon)
Score: 169

GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 257

GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 184

GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 345

GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTAgtaaatataa ... gcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctatatttaatttaagatcacacgttaatgcttgaaccttctgcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC
                         cgttaat  putative branch site (score: 345)
                                       ccttctgc  putative PPT
     atatttaatttaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatataataagtttgttaagcatctatgaattatgattctatttatgttattattatgttctatatttaatttaagatcacacgttaatgcttgaaccttctgcacttacagTTCCACATTCTTTTCTGCGTATTTTCTGCTGTGGCTCCTCCTGTTGTATTTGAAGGAAAATCATTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA