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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttagcctgctgataactttctgtgtgattctactgattatatctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG

Basic information

species Zea mays
transcript GRMZM2G149994_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149994_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g42110.1 (Oryza sativa), 3'ss of exon 10
---------gtactgttagcctgctgataactttctg-tgtgattctactgattatatct---acatgtatattc-----actagaag--------gcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG
           |   ||||  ||  |||  | |||   ||||| ||| ||  | ||||||   | |||    |||     |||| ||         |||||  ||  | ||||||||||| ||||||| |||||| |||||||||||||||||||||||||||||| |||| |||||||||||||||| |
gtacctcttacatatttagattgacgatggcattcaaatgtgactctccttgtcatatctcatatatgccctttctttgtactaaaaaagtatcttgcaatttttgatgtagGGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTCGATATG

upper sequence: GRMZM2G149994_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g31220.1 (Oryza sativa), 3'ss of exon 6
---------gtactgttagcctgctgataactttctg-tgtgattctactgattatatct---acatgtatattc-----actagaag--------gcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG
           |   ||||  ||  |||  | |||   ||||| ||| ||  | ||||||   | |||    |||     |||| ||         |||||  ||  | ||||||||||| ||||||| |||||| |||||||||||||||||||||||||||||| |||| ||||||||||| |||| |
gtacctcttacatatttagattgacgatggcattcaaatgtgactctccttgtcatatctcatatatgccctttctttgtactaaaaaagtatcttgcaatttttgatgtagGGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTTGATATG

upper sequence: GRMZM2G149994_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------------------gtactgttagcctgctgataactttctgt--gtgattctactgattatat-----ctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG
                                                                                                  |||  ||  | |||| | |    | |||  ||   || || |     ||   ||  |||| ||||||     ||  |||||| |||||||| | || ||||  ||||| ||||||||  |||||||||||||||| ||  ||||||| |||||||| |||  |
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttatt-ttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG

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|24934695|gb|CA452913.1|CA452913
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTGGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|76015203|gb|DT942373.1|DT942373
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|37391984|gb|CF633237.1|CF633237
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|211033356|gb|FL442938.1|FL442938
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAAAGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|67026000|gb|CO454749.1|CO454749
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|24934696|gb|CA452914.1|CA452914
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTGGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|67018676|gb|CO447425.1|CO447425
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|24961608|gb|CA483609.1|CA483609
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTGGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|33092600|gb|CF052594.1|CF052594
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|24773369|gb|CA408623.1|CA408623
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTGGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|24773164|gb|CA408418.1|CA408418
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTGGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
EST: gi|4609489|gb|AI600328.1|AI600328
EST:     GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACG                         GGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT
genomic: GACTTTTGTCGACTTTATTGACCGAAATGGATGGTTTAGAACTGGCTACGgtactgttag ... ctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctactgattatatctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG
     tactgat  putative branch site (score: 2)
                                           tccttttttt  putative PPT
          attatatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttagcctgctgataactttctgtgtgattctactgattatatctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT