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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagactttctttttctttttcttcttttttttttaattgcacttgcttgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG

Basic information

species Zea mays
transcript GRMZM2G127379_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03300.1 (Oryza sativa), 3'ss of exon 2
gtgagtgagactttctttttctttttcttcttttttttttaattgcact--tgcttgcacggctccagac-ctgactgaagcgtttcgcatggtt--tcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGG-CGG-
 ||||   |  ||  | ||  | | | || | ||||||  ||  |   |   | |||||||  || |     ||  |   || |||   || ||   ||||||||||||||||||||||||||| |||||||||||||||||||| ||| | |  ||          || || || | ||||  | |  | ||| ||  | | 
-tgagcttgttttattcttggtatatattttattttttagaaaagggttaaagtttgcacgcttctaattattgtttactgcatttgtgattgtccatcagCTGGACGACTGGGTGCTGTGCAGAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAG--GAATCAACCGTCGAACAGC

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03040.1 (Oryza sativa), 3'ss of exon 2
-gtgagtgagactttctttttctttttcttcttttttttttaattgcacttgcttgcacggctccagac-ctgactgaagcgtttc--gcatggtt--tcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG--
  ||| ||||  | | ||||  | ||| ||  ||     | |||    |  | ||||||   || |     ||  |   || |||     || |||  ||||||||||||||||||||||||||| |||||||||||||||||||| ||| | |  ||          || || || | ||||  |||  | ||| ||  |   
gttgattgagcttgtgttttattctttatt--ttaaaaataaataaagcaagtttgcacacttctaattattgtttactgcatttgtgatattgttcatcagCTGGACGACTGGGTGCTGTGCAGAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAG--GGATCAACCGTCGATGAAC

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03300.2 (Oryza sativa), 3'ss of exon 2
gtgagtgagactttctttttctttttcttcttttttttttaattgcacttgcttgcacggctccagac-ctgactgaagcgtttcgcatggtt--tcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGG-CGG------------------------
                       | | || ||||||    ||  |     | |||||||  || |     ||  |   || |||   || ||   ||||||||||||||||||||||||||| |||||||||||||||||||| ||| | |  ||          || || || | ||||  | |  | ||| ||  | |                        
----------------------atattttattttttagaaaagggttaaagtttgcacgcttctaattattgtttactgcatttgtgattgtccatcagctggacgactgggtgctgtgcagAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAG--GAATCAACCGTCGAACAGCTTGAAGACATCCATGACAACAAC

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ36823 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgagactttctttttctttttcttcttttttttttaattgcacttg-cttgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGAC-TGGGTGCTGTGCAGGATCCACAAGAAG----AGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCA-TGAGCAC-GAGCAGGAGGAGCCGGCGGCGG---
                   |   ||||   |  |     || |||||   | | ||||         |    ||  ||         |       |||| ||   | || ||| | |  |  | | |            |||| | | | |   | |||| |  |  |||  | || |  | | || |||    | |   |  |   
------------------gtaagtttcaattcctccaagtagttgcataagtcctgcatattggggaaaaaaacaaaaaaaaaaaaaaaaaagagagctcgagctcatgagtggtattaaaaaccgatggcttactttggcaa-gctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27849 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgagactttctttttctttttcttcttttttttttaattgcacttgcttgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGAC-TGGGTGCTGTGCAGGATCCACAAGAAG----AGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCA-TGAGCAC-GAGCAGGAGGAGCCGGCGGCGG---
      |  | ||||  || ||     |  ||   |       ||||  |    | |      || |    ||  ||         |  |    |||  ||   | || ||| | |  |  | | |            |||| | | | |   | |||| |  |  |||  | || |  | | || |||    | |   |  |   
------gtaagtttcaattcctccaagtagttgcatccagtcctgcatat-tggggaaaaaaacaaaaaaaacaaaaaaaaaaaaaaaagaaagagcgagagctcgtgagtggtattaaaaaccgatggcttactttggcaa-gctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgagactttctttttctttttcttcttttttttttaattgc--acttgct-tgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG
                                  |||   |   ||  ||| | | |  || | |   |||     |  |   || |   |  ||||||||||||||||||||||||||| | ||  |||| ||||                                                               
---------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttga--cttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------

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|148976344|gb|EE025927.2|EE025927
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|76020928|gb|DT948098.1|DT948098
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|71767924|gb|DR965861.1|DR965861
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCACCGATTTTCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|148941938|gb|EC886925.2|EC886925
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCCACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|88757969|gb|DY542110.1|DY542110
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|76926936|gb|DV171063.1|DV171063
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|74238117|gb|DT646031.1|DT646031
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGANG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACG
EST: gi|148932878|gb|EE285642.2|EE285642
EST:     AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGG                         CTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
genomic: AGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAG
EST: gi|211365730|gb|FL263991.1|FL263991
EST:     TGGCAGCACCAGGCGCATAGTGTCTTCCCTCCTCGTCGTCCTCCCTGAGG                         CTGGACGACTGGGTGGCTTTGCAGGATTCACCAGAA
genomic: GGGCAGCACCAGGCGCAGAGTGTCTTCC-TCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTG-CTGTGCAGGATCCACAAGAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 196

CTGGATCATGCACGAGTACCGCCTCTCGGGCGCGGCGGACGACGACTGCAAGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 109

CTGGATCATGCACGAGTACCGCCTCTCGGGCGCGGCGGACGACGACTGCAAGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

CTGGATCATGCACGAGTACCGCCTCTCGGGCGCGGCGGACGACGACTGCAAGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 30

CTGGATCATGCACGAGTACCGCCTCTCGGGCGCGGCGGACGACGACTGCAAGGGCAGCACCAGGCGCAGAGTGTCTTCCTCCTCGTCGTCCTCCATGAGGgtgagtgaga ... atggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcacttgcttgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG
                         acctgac  putative branch site (score: 30)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagactttctttttctttttcttcttttttttttaattgcacttgcttgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG