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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacattgttgacagactggagtgcttactaaatcctgctatatgcatatttccccttagtttattctacatgttttacatgcttgtcttatgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACGAAGAAATGTCCTCCACAT

Basic information

species Zea mays
transcript GRMZM2G079452_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079452_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g23790.2 (Oryza sativa), 3'ss of exon 2
agacattgttgacagactggagtgcttactaaatc-ctgctatatgcatatttccccttagtttattctacatgttttacatgcttgtcttatga--tggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACGAAGAAATGTCCTCCACAT
  | |||  | |   | |    | | ||  | ||| ||    | |  |  | |   |   | ||  ||||   |  |||||     || || | |  ||||||||||| ||| | ||||||||| | |||||||||||||| || ||||| || || ||||| |||||||||
--agattaattaataattattct-catatcatatctcttgagtcttgacctgttttccatgctttgtctattggccttacacatcagtttttttaactggcagCGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACAAAAAAATGCCCTCCACAT
















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|71311108|gb|DR791867.1|DR791867
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|76289326|gb|DV028894.1|DV028894
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|149112959|gb|EE295744.2|EE295744
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|76012260|gb|DT939430.1|DT939430
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|71429968|gb|DR811018.1|DR811018
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|149107701|gb|EE189577.2|EE189577
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|71774790|gb|DR972668.1|DR972668
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|211518577|gb|FL052083.1|FL052083
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGRCACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTA
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTA
EST: gi|211518580|gb|FL052086.1|FL052086
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|78090608|gb|DV518982.1|DV518982
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|211518576|gb|FL052082.1|FL052082
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|91051210|gb|EB161628.1|EB161628
EST:     TGGCACTTGATTACATGATAAAACTTGCACAGAAGGACACAAATGATGAA                         CGTAAGTCTAT
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTAT
EST: gi|149096864|gb|EE182658.2|EE182658
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|18963872|gb|BM660677.1|BM660677
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGGGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
EST: gi|71444932|gb|DR825982.1|DR825982
EST:     TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAG                         CGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG
genomic: TGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggta ... atgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttccccttagtttattctacatgttttacatgcttgtcttatgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACGAAGAAATGTCCTCCACAT
           ttagtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacattgttgacagactggagtgcttactaaatcctgctatatgcatatttccccttagtttattctacatgttttacatgcttgtcttatgatggcagCGTAAGTCTATTCTTGAGGTAATTAAGCAGACAGTGCTAGACCATCTGACGAAGAAATGTCCTCCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - -ttgttga
- - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - cctgcta
- - - - - - - - - - - - - - - - - - - - - atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgc