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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaaccgcctgttgatcccggtctctttcttccccccttcaacagctggagtatttgtctctcgtgatcggtgaaattcatctgatgtatcctgaa...

Basic information

species Zea mays
transcript GRMZM5G870446_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870446_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g04790.1 (Oryza sativa), 5'ss of exon 1
GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaaccgcctgttgatcccggtctctttcttccccccttcaacagctgga-gtatttgtctctcgtgatcggtgaaattcatctgatgtatcctgaa
| ||  ||||| | ||||||||||||||||||||| | |||||||||||||||||||| ||||| ||||| || |||||||||||||||||||||||||||||||       |  ||   |||  || ||   || |    ||  |   ||  |  |||||   | |  |      |    ||  | |||  ||   ||  
GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagcccttctcacttttcccctctcgctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg-

upper sequence: GRMZM5G870446_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT4G04020.1 (Arabidopsis thaliana), 5'ss of exon 1
GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaaccgcctgttgatcccggtctctttcttccccccttcaacagctggagtatttgtctctcgtgatcggtgaaattcatctgatgtatcctgaa-------
| ||  || |    ||||||||||| ||||||||| |    ||||| || || || |||| |||||| |||   |||||||||||||| |||||||||||||||| |     || ||  | | | |    | ||   | |       |     ||| |||||| |     ||   | |||    |    | ||  ||          
GAGCTGAGATCAGCGAGCTCATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCTAACGAAGCTCTGTTTCTCCTCAACGGCAAATGGATCCTCGCgtaagta-----cttttagttctgatactctcctaggcacggcatgtaatattagt-tttgtcccaaac-attactcaaaccggtgatctctaagcttcgtctagga
















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|211138814|gb|FL422225.1|FL422225
EST:     GGCGCCTACCGAAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCCGC                         GTACACATCAT
genomic: GGCGCCTACCGAA-GCGCTGACGCTCCTCAACGGCAAGTGGATCCTC-GCgtaagaaacc ... gtgatttcagGTACACATCAT
EST: gi|211290009|gb|FL375492.1|FL375492
EST:     CGGCGCCTACCNGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATT
genomic: CGGCGCCTACC-GAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATT
EST: gi|211048945|gb|FL421711.1|FL421711
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTT
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTT
EST: gi|211321193|gb|FL380421.1|FL380421
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGGGAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
EST: gi|88755855|gb|DY539996.1|DY539996
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
EST: gi|211113241|gb|FL096526.1|FL096526
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
EST: gi|149073572|gb|EE161875.2|EE161875
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCC
EST: gi|211026990|gb|FL377492.1|FL377492
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTC
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTC
EST: gi|93014092|gb|EB639612.1|EB639612
EST:     CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAA
genomic: CCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAA
EST: gi|211334023|gb|FL370158.1|FL370158
EST:     CGGCGCCTACCGAAGCGCTGACGCTCCCTCAACGGCAAGTGGATCCTCGC                         GTACACATCATTTTCCCAACTGTTC
genomic: CGGCGCCTACCGAAGCGCTGACGCTCC-TCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTC

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), 45 (downstream exon)
Score: 14

GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCCAGCGCTGGTGAAGGTGGAGGAAATATCACAGACCATTGATTCCAAGAAC


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

GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCCAGCGCTGGTGAAGGTGGAGGAAATATCACAGACCATTGATTCCAAGAAC


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

GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCCAGCGCTGGTGAAGGTGGAGGAAATATCACAGACCATTGATTCCAAGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaacc ... gtgatttcagGTACACATCATTTTCCCAACTGTTCCCACTGTTGGAGTTTGGAAAGCTGCCAGCGCTGGTGAAGGTGGAGGAAATATCACAGACCATTGATTCCAAGAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaaccgcctgttgatcccggtctctttcttccccccttcaacagctggagtatttgtctctcgtgatcggtgaaattcatctgatgtatcctgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct