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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G141903_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtacatgtaaaaatgctctccctaccttaatactatcaga----cacaatttaggggggag--ggttgacattttgtcagtgctttcgtgttt--ttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
    ||| || |||        ||  ||  |  ||  |    ||    |||| |||   |    |  | ||  | |||||     | ||| | | ||  || |   || | | ||    |||    ||  ||||||||||||| ||||| |||||||||||||| ||||||||  |||| ||||||||||||||||| |||
----gtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattga--agtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtacatgtaaaaatgctctccctaccttaatacta-tcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtt-tgctga-----ctg-atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
    ||| | |||     ||  |   ||  |||| |||| ||   |   |||||  |        |||  | |  || | | |||  |  || |  |    |    ||| ||||||      ||  ||| ||||||| ||||| ||||| |||||||||||||| ||||||||  |||| || |||||||||||||| |||
----gta-acgtatcctcgcagtt--tattttaacactaatctttcgttatttacagttttcccatgatgtgt-atctgcgattttttcattctgaagtacttctcgttatgctgaagagattgcgtggttgcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgc-agATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                      |    |      |       |||    ||| |   | |  |||| |||| |||      |        ||  ||  || |  || | |  ||    ||| ||  |||| || |||||||| || || || |||||||| |||||  |||| |||||||||||||||||||||
---------------------gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgtttacaatcaaccagcttccta--tagacctgatagtcgatcattgggtgttagATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG

upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                                                                         || |||  |||   || |  | |    ||  || |  |   |  |      |||||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||
-------------------------------------------------------------------------gtgagtctttt---gtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

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|149107620|gb|EE189502.2|EE189502
EST:     GTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: GTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|18964717|gb|BM661166.1|BM661166
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACNT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|78027572|gb|DV495959.1|DV495959
EST:     TGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: TGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|76925598|gb|DV170499.1|DV170499
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|60353291|gb|DN220264.1|DN220264
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|60400467|gb|DN233274.1|DN233274
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|5895649|gb|AW036895.1|AW036895
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|60344732|gb|DN211705.1|DN211705
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|19351815|gb|BM896347.1|BM896347
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|32849417|gb|CD989098.1|CD989098
EST:     ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacat ... atggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                tttttttacctatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggagggttgacattttgtcagtgctttcgtgtttttttacctatatatgtttgctgactgatggctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG