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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacatttcagaagctatctcaaactcaatcggtttcaactttcagaaaggtccataataataacactgtttctgtgggaaaaaaattcacaccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCACATTAGCAGCAGAGACAG

Basic information

species Zea mays
transcript GRMZM2G152447_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152447_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 5
gttacatttcagaagctatctcaaactcaatcggtttcaactttcagaaa--ggtccataataataacactgtttctgtgggaaaaaaattcacaccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCACATTAGCAGCAGAGACAG
           | | |  |   |||    |    ||| | |||  |  ||  |||     |||  | ||    |||  ||  |   |   | |   |   ||||| || || ||||| |||||||||||||| || |||||||| ||||||||||| ||||||||| ||||
-----------gtaacactgataaaaagtagtactttaatcttctaccaattggtttcgcatatgagca----ttcgatgaaatttacgatgatttca--cagGAAAACGGTGTCGATTTCTACATCAATGGGCATGATCACTGCCTGGAGCACATCAGCAGCAGAAACAG
















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|50328960|gb|CO524086.1|CO524086
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTTTACATCAATGGACACGATCACTGTTTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|211512568|gb|FL110029.1|FL110029
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|71436322|gb|DR817372.1|DR817372
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTTTACATCAATGGACACGATCACTGTTTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|18169298|gb|BM339138.1|BM339138
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|116817885|gb|EC860795.1|EC860795
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|24934165|gb|CA452383.1|CA452383
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|149107456|gb|EE189334.2|EE189334
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|22491632|gb|BU051555.1|BU051555
EST:     AGCACGGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGGCACGAT
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGAT
EST: gi|78109968|gb|DV528383.1|DV528383
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTTTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|78109969|gb|DV528384.1|DV528384
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|78086366|gb|DV514759.1|DV514759
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTTTACATCAATGGACACGATCACTTTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|76288593|gb|DV028161.1|DV028161
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCTATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|211512569|gb|FL110030.1|FL110030
EST:     AGCACGGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGGCACGATCACTGCCTGGAACAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|78110599|gb|DV529007.1|DV529007
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|71312265|gb|DR792656.1|DR792656
EST:     AGCACAGGGACACCGAGGAGCTTCTGGA-TTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGAACACGATCACTGT
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGT
EST: gi|116828633|gb|EC859889.1|EC859889
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|101394597|gb|EB819233.1|EB819233
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
EST: gi|56461959|gb|CK986257.1|CK986257
EST:     AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAG                         GACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC
genomic: AGCACAGGGACACCGAGGAGCTTCTGGAATTACTACTTCCAGTCCTCAAGgttacatttc ... caccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggtccataataataacactgtttctgtgggaaaaaaattcacaccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCACATTAGCAGCAGAGACAG
             taataac  putative branch site (score: 1)
         ataataataacact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacatttcagaagctatctcaaactcaatcggtttcaactttcagaaaggtccataataataacactgtttctgtgggaaaaaaattcacaccgttcagGACAATGGCGTCGACTTCTACATCAATGGACACGATCACTGTCTGGAGCACATTAGCAGCAGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA