Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccgaatcctcaaaattttatgagccacatacactgaagttactgatagttccaaaggttcattgatggtgatgaaggctaagatactgttcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT

Basic information

species Zea mays
transcript GRMZM2G408989_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 2
tccgaatcctcaaaattttatgagccacatacactgaagttactgatagttc-caaaggttcattgatg-gtgatgaaggctaagatactgttcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT
 | ||||  |  | | |  |  ||| ||||      ||     | ||  | |    |  ||  ||  |  |  |   |   ||| ||| | |  |  | ||||| ||||||||||||||||| || || |||||||||||||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||
-cagaatgatgcatagtaaagtagc-acattagtaaaacacggtcatgttgcatttacatttgttagtatgatacacaaattaacataatttcaccgttcagATCTGCTGGGCATTTTCGATTTACTTGGAGGCAGTGGCAATTCTCCCTCAGTTAGTTTTGCTGCAGAGAAGTAGAAATGTGGACAACTTGACTGGACAAT
















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|211036981|gb|FL384634.1|FL384634
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATGTGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|91871430|gb|EB401416.1|EB401416
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|50330722|gb|CO525848.1|CO525848
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|60344375|gb|DN211348.1|DN211348
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|31354771|gb|CD439128.1|CD439128
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|32912106|gb|CF016918.1|CF016918
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACA
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGA-Ggtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACA
EST: gi|60342889|gb|DN209862.1|DN209862
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|211379193|gb|FL377345.1|FL377345
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     CTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
EST: gi|78080744|gb|DV509156.1|DV509156
EST:     CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAG                         ATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG
genomic: CCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAG

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), 48 (downstream exon)
Score: 118

GACTTACGACAAGGAGCAGGACACCTTCCGCCACGCGGTGCTCGTCGCCGCCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

GACTTACGACAAGGAGCAGGACACCTTCCGCCACGCGGTGCTCGTCGCCGCCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 66

GACTTACGACAAGGAGCAGGACACCTTCCGCCACGCGGTGCTCGTCGCCGCCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GACTTACGACAAGGAGCAGGACACCTTCCGCCACGCGGTGCTCGTCGCCGCCGCGTTCCTGCTCGCGCTGATGTTCCACGACCGGTTCACCTTCCGAGAGgtgatgtttt ... tcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttccaaaggttcattgatggtgatgaaggctaagatactgttcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT
                                         ctgttccttt  CT-rich tract
                                  taagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccgaatcctcaaaattttatgagccacatacactgaagttactgatagttccaaaggttcattgatggtgatgaaggctaagatactgttcctttgcagATATGCTGGGCATTTTCGATCTATTTAGAGGCAGTGGCAATTCTCCCACAGTTAGTGTTACTCCAGAGAAGCAGAAATGTGGATAACTTAACTGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - -catacac
- - - - - - - - - - - - - - - - - - - - tactgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg