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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattttcttatcatctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gtgaattttcttatcatctgaatgagaatgaaagagccg-tatcaatatctgctgtaatctgatagcgtg--ggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
||||| |||| ||  | ||||||||     |||  | |  | | || |  ||    ||||| ||  ||||    |  |||||||||||||| |||||| |||| || || |||||||| |||||||||||||| || || || || || |||||||| | |||||||||||| ||||| ||
gtgaagtttcgta--acctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
-gtgaattttcttatc-atctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttg--cagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
  |  |||  | | |  || | | | |  |  || ||       |    | |         |  || |  |   |   | |||||  ||||||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||||||||| ||
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgc-tttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtgaattttcttatcatctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttg--cagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
|| |  || |      | || ||||| |   ||   | |   |  ||||   |    | |  || |  |       | |||||  ||||||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||| ||||| ||
gttagattccc--atgtttggatgagcaatgaatttctgctgctttatcaagt----tatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------gtgaattttcttatcatctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
              |  | |    || ||      |      | |   |    | |   |   | | ||||      || |  | |  |    | |||||||||||||||||||||||| ||| ||||| |||||||| |||||||||||||| || || ||||| || |  ||||| ||||||||||||||
ttctgttatcagctgcaattgggattgtcggtgagaaacagttaagctactaattttgttcaatacagtaacaattcagtggagctttctgtgtctgcagCTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
------gtga-attttcttatc--atctgaatgagaatgaaagagccgtatcaatatctgctgta-atctgatagcg-----tgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
      || | ||| ||||| |  ||   ||||  |  || |  |  | |||   |  || || | || || |  |      |   | | | ||||| |||||||||||| | ||||||||||| || ||||| ||||| |||||||| || || || ||||||||    | |||||||||||||||||| ||
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaag-atctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

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|211227826|gb|FL399539.1|FL399539
EST:     ATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAG                         CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGC
genomic: ATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAGgtgaattttc ... tcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGC
EST: gi|71772341|gb|DR970277.1|DR970277
EST:     ATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAG                         CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGC
genomic: ATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAGgtgaattttc ... tcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG
                                     gggtaac  putative branch site (score: 3)
                                           catctttt  CT-rich tract
        tatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattttcttatcatctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA