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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGGATGTTTGTGCAAAACCTCCTACCGAGCGCCTCTTCCTTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctccaactcgtttttctggcctcgtggatatttctttgtgcctgtaatctgggtatggtataatgcttaccatatcagctggatgttccaatgt...

Basic information

species Zea mays
transcript GRMZM2G138053_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138053_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g06730.t01 (Vitis vinifera), 5'ss of exon 4
--------TCAAGGATGTTTGTGCAAAACCTCCTACCGAGCGCCTCTTCCTTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctccaactcgtttttctggcctcgtggatatttctttgtgcctgtaatctgggtatggtataatgcttac-catatcagctggatgttccaatgt
        | || ||||| ||||  || ||||| || ||||||||||||||||| || ||||| | ||| ||||| || || || || ||||||||||||||           ||   ||| | ||  | |  | |    |||||  || || | |  |||   ||  |  |  ||  |  || | |         |||  
CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggatgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata-
















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|58029986|gb|CX725413.1|CX725413
EST:     TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|50329775|gb|CO524901.1|CO524901
EST:     TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|4885897|gb|AI677017.1|AI677017
EST:     TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|88750361|gb|DY534502.1|DY534502
EST:     TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|113795695|gb|DW912380.1|DW912380
EST:     GGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
genomic: GGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|116818193|gb|EC861175.1|EC861175
EST:     TTGACCAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGGGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA
EST: gi|116817866|gb|EC860776.1|EC860776
EST:     TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAG                         GGGTTGCTTGAAAACACGGAGAAAGACAGAGTGGGGAGGTTGATTAGACTA
genomic: TTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctcc ... atcatcccagGGGTTGCTTGAAAACACGGAGAAAGACAGAGTGAGGAGGTTGATTAGACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGGATGTTTGTGCAAAACCTCCTACCGAGCGCCTCTTCCTTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctccaactcgtttttctggcctcgtggatatttctttgtgcctgtaatctgggtatggtataatgcttaccatatcagctggatgttccaatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG