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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtagaagatctatctcttggctggcaacaattatctatgtacagactacaaaacgtaacattgatatgacgatatgttaactgagatactcacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG

Basic information

species Zea mays
transcript GRMZM2G168506_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 3
gtagtgtagaagatctatctcttggc-tggcaacaattatctatgtacagactacaaaacgtaacattgatatgacgatatgttaactgagatactcacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG
    ||    ||||  ||    |  | || |   |  |   | |||   |  |||| |     ||||  | |  || |  | | ||||||  || |||  || ||||| ||||| ||| | |||||||||||||||||  | |||||||| || ||||||||||
--gatgagtcagattaataatctaccgtgcctttagctgattgtgtctgg--tacagagtaccacatgta-acaactaagt-tgaactgaactattcatttggcagGACGAAGTTGTAGCTAGGATAGAGGAGAGGATTGCAGCTTGGACGTTCCTTCCACCAG
















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|50334167|gb|CO529293.1|CO529293
EST:     AGGTTCAAAATGAAGCCTCAACATTTCATGGCTTATGTGGAATGAGTAAT                         GATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTT
genomic: AGGTTCAAAATGAAGCCTCAACATTTCATGGCTTATGTGGAATGAGTAATgtagtgtaga ... cacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTT




















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 3 RNA-Seq libraries.


Block sizes: 17 (upstream exon), 33 (downstream exon)
Score: 1

GGAAAAAGACTGGGAAGGCCCCATGGTCCTAGGTTCAAAATGAAGCCTCAACATTTCATGGCTTATGTGGAATGAGTAATgtagtgtaga ... cacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG


Block sizes: 32 (upstream exon), 28 (downstream exon)
Score: 2

GGAAAAAGACTGGGAAGGCCCCATGGTCCTAGGTTCAAAATGAAGCCTCAACATTTCATGGCTTATGTGGAATGAGTAATgtagtgtaga ... cacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 2

GGAAAAAGACTGGGAAGGCCCCATGGTCCTAGGTTCAAAATGAAGCCTCAACATTTCATGGCTTATGTGGAATGAGTAATgtagtgtaga ... cacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaaaacgtaacattgatatgacgatatgttaactgagatactcacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG
                                         tactcac  putative branch site (score: 2)
                                           ctcacct  CT-rich tract
                          atatgttaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtagaagatctatctcttggctggcaacaattatctatgtacagactacaaaacgtaacattgatatgacgatatgttaactgagatactcacctgtcagGATGAAGTAGTAACGAGGATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT