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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtattatactatccgagtgaagcctgacgaccatacctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG

Basic information

species Zea mays
transcript GRMZM2G037923_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 13
gtacagtattatactatccgagtgaagcctgacgacca-tacctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
     |||   ||| ||| |  ||| |  |||  |  | ||| |    |||| ||| ||  ||   ||  | ||||||||||||  |||||||| |||||||||||||||| ||||||||||| |  | ||||||||||||||| ||||||||| | ||||| || || || ||||| ||||||||||
-----gtaaagtacaatctgt-tgaggtgtgataattagtacttgg--attatttgttt--gctgagagtcctaactctgtttc-aattatacatagGACTGGATAATGGATCAGTGGGAGAAGAATTTCTACATAACAGCAATAGCTGGATCAGCTAACGGAAGTTCTTTAGTTGTGATGTCCAAAG

upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13
-------------gtacagtattatactatccgagtgaagcctgacgaccatacctaa-------taattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
                  |  |||||  || |   |   |    |  |  |    | |       ||| |||||||| |      |  | |   ||    || ||||    | ||||||||||| |||||||||||||||||||  ||||| || |   |||| |||||  ||   || || || || |||||||||||||||||||
gtgggttttttcttccttgatttatataattcatcttttgttaaataaatacgtatgagttaaattaaataattgatgtcttggtgctgggctgctggcattttgatc--tctcagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG
















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|32869986|gb|CF009668.1|CF009668
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|21432270|gb|BQ547760.1|BQ547760
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGTCAATTGC
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAG-CAATTGC
EST: gi|22473314|gb|BU037794.1|BU037794
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|33097651|gb|CF057611.1|CF057611
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|33096688|gb|CF056682.1|CF056682
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|22713641|gb|BU197414.1|BU197414
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|22545509|gb|BU097868.1|BU097868
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|31355521|gb|CD439878.1|CD439878
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|21987385|gb|BQ778913.1|BQ778913
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|87156443|gb|DY401232.1|DY401232
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|26559413|gb|CA831648.1|CA831648
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
EST: gi|31356845|gb|CD441202.1|CD441202
EST:     CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAG                         GACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT
genomic: CTGGTTTCTGTTCTCAGGTTTATGAGCTCTCACCAGTTTTCCTCCACAAGgtacagtatt ... ttatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG
                                       ttctgat  putative branch site (score: 3)
     aattaattgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtattatactatccgagtgaagcctgacgaccatacctaataattaattgatttagccaggaagcgtaactctgtttctgattatacacagGACTGGATAATGGAGCAGTGGGAGAAAAGCTACTACATAACAGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA