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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca...

Basic information

species Zea mays
transcript GRMZM2G145213_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g39540.1 (Oryza sativa), 5'ss of exon 1
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca-----
                                    ||| ||||| |||||||| | ||| | ||||||||||| ||||||||||||||| | ||||||||| | || |    |     | |    ||||  ||  |       |||  | | |   | ||||   |  ||| |    |||||  |         |||       
------------------------------------ATGAAGGAGAGGGAGAAGGTGGTGCGACTGGCCAAGCTCGCCGAGCAGGCGGAGAGATACGACGgt-atggctgggatgggatctcggattgctggattgttcgattgcgcgttgctgttgtgcagttcttgttcttg----gttctttgcatttgggggttgggggga

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 5'ss of exon 1
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcg--ttgttctcggtgcccttcagttca
    | || ||   ||| |       |  |     |  | ||||||| ||||  |  |||| | |||||||||| ||||||||||||||||| ||||| |||| | | ||| |      |   ||  |  |  |  |  |||          |    |      || | |   | |  |||   |  |||| |  |  |   
TTTTGTGTGGTTTAGAGTGCTGTCAAGATGAGCACGGAGAAGGAGCGTGAGAGCCAGGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGATACGATGgtgcgtgttcttgagag-actgactgagagtgcttttgttgctgtttttgttgtcgttgtttcttcgagttcggtggtttgaatttcgtgctcgacgatgg-

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 1
GGGAGAGTTGTGGGGAGGGGATCGGC---GGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccc-tctgcttaataataatgccccgccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca-
    ||||||   |     | |||||   |  |   | |  | ||||||| ||||     |||| | |||||||||| ||||||||||||||||| |||||||||  | | |    || | |  |   | ||  |  |  |  ||    |   |       |    | | |  | |      | || ||  ||   |   || | 
---GGAGTTGCTTGCGCAAGTTCGGCCAGGATGAGTGCGGAGAAGGAGCGCGAGAGCTATGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGTTACGACGgtacgtgcttaattttttgtcctggtgtgtgtgtttgtt-tgttttgttttgttttgttttgttttttttttttttccagatcgcga-gcttgttgtttgaa

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 5'ss of exon 1
GGGAGAGTTGTGG--GGAGGGGATCGGCGGCGGAGGAGATGGAG---GAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcgttgttc-tcggtgcccttcagttca
      || ||||  |   | | | |||   |  |   | ||||   ||||| ||||     |||| | |||||||||| ||||||||||||||||| ||||| |||| | |     | ||              |  |  |  |  ||    |   ||   |   |    |  ||  | ||| ||  |   |    |    ||  
-----TGTCGTGGACGAGTGTGCTAGGCCAAGATGAGTACGGAGAAGGAGCGCGAGAGCTATGTGTACATGGCCAAGCTCGCCGAGCAGGCGGAGCGTTACGATGgtgtgtgtgtgtgctcgatatgttaacatgtttttcttctttccattagcttggtttttgtggagtttttcgggagttatttgtttatttattattatta-

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ35972 (Selaginella moellendorffii), 5'ss of exon 1
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccg---ccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca
                             ||    |  | ||||||| ||     | || |   ||||||||||||||||||| || ||||| ||||||||||||        |    |||       |         || || ||   | || || ||||   |||| |   |  ||                         
---------------------------ATGGGAATGGAGAAGGAGCGCGAATGCTTTGTCTATATGGCCAAGCTTGCCGAGCAAGCAGAGCGCTACGACGgtgagctcctggatcgatgcgataatctcgcgccttcgattcctcggatctgtgcgtgactcttgtctatttccccgcag-----------------------

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ36243 (Selaginella moellendorffii), 5'ss of exon 1
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccg---ccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca
                                   |  | ||||||| ||     | || |   ||||||||||||||||||| || ||||| ||||||||||||        |    |||       |         || || ||   | ||  | ||||   |||| |   |  ||                         
---------------------------------ATGGAGAAGGAGCGCGAATGCTTTGTCTATATGGCCAAGCTTGCCGAGCAAGCAGAGCGCTACGACGgtgagctcctggatcgatgcgataatctcgcgccttcgatccctcggatctgtgtgtgactcttgtctatttccccgcag-----------------------

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|78109295|gb|DV527711.1|DV527711
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|22935751|gb|BU572026.1|BU572026
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|74234408|gb|DT642322.1|DT642322
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|211368301|gb|FL143994.1|FL143994
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGASSGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|211368297|gb|FL143990.1|FL143990
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGA-SGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|74240176|gb|DT648090.1|DT648090
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|211365651|gb|FL143989.1|FL143989
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|211368299|gb|FL143992.1|FL143992
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|71302156|gb|DR787186.1|DR787186
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|5566988|gb|AI881899.1|AI881899
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|31353761|gb|CD438118.1|CD438118
EST:     AAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCTTCTC-GAGAGGAACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: AAGCTCGTGTGCCTGGCCAAGCTTGCCGAGC-AGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|20300796|gb|BQ163739.1|BQ163739
EST:     GAAGCTCGTG-GCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|78093195|gb|DV521569.1|DV521569
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|67020921|gb|CO449670.1|CO449670
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|101382257|gb|EB813184.1|EB813184
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|44681886|gb|CK786934.1|CK786934
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|71448133|gb|DR829183.1|DR829183
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|211368298|gb|FL143991.1|FL143991
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGA-CGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
EST: gi|71444597|gb|DR825647.1|DR825647
EST:     GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACG                         ATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG
genomic: GAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTG

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), 38 (downstream exon)
Score: 132

GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTGCTGAAGAAAGGCATTTGTTCTCAGTTGGTTTCAAGAACACTATTGGAGC


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 77

GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTGCTGAAGAAAGGCATTTGTTCTCAGTTGGTTTCAAGAACACTATTGGAGC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 143

GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTGCTGAAGAAAGGCATTTGTTCTCAGTTGGTTTCAAGAACACTATTGGAGC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 124

GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatc ... attatgtcagATATGGTGGAATTCATGAAGAATCTTGCTAGGATGGACGTGGATATGAGTGCTGAAGAAAGGCATTTGTTCTCAGTTGGTTTCAAGAACACTATTGGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAGAGTTGTGGGGAGGGGATCGGCGGCGGAGGAGATGGAGGAGCGGGAGAAGCTCGTGTGCCTGGCCAAGCTTGCCGAGCAGGCGGAGCGGTACGACGgtgagggatctcgttctcgcgccctctgcttaataataatgccccgccgtacgggactacagtctctactctagcgttgttctcggtgcccttcagttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgcc