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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcgtccgttgtgggaaaaaagttctggatttgaacatggatagtctgttgccttctttcttctgtaatttactgtttcttttcgtgttgttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG

Basic information

species Zea mays
transcript GRMZM2G134738_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 3
gttcgtccgttgtgggaaaaaagt-tctggatttg--aacatggatagtctgttgccttctttcttctgtaatttactg-tttcttttcgtgttgttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG
     |      ||| | |  ||| |||  ||||   | | || |   ||  |||    |  | |  ||| ||| |    |||  | | |||||   |||||||||||  |||||||||||||| || |||||||||||| ||||||| |||||||||||||| || || |
--atctgaaccatggcacattagtctcttcatttattatcttgcagcatcatttgagcaccatgtcatgttattcatcaatttgctatggtgtta--cctgcagGAGGCCCCAGCTGTCATTGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG
















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|60357675|gb|DN224648.1|DN224648
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     GGAAGAAGCGGTTCGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|29130310|gb|CB381014.1|CB381014
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGACGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|161588036|gb|EY962533.1|EY962533
EST:     CGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: CGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     GAGGAAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GAAG-AAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTATTTTT                         GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT
genomic: GGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAGgttagttcgc ... gttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgccttctttcttctgtaatttactgtttcttttcgtgttgttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG
                                           ttgttcct  CT-rich tract
                   tgtaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtccgttgtgggaaaaaagttctggatttgaacatggatagtctgttgccttctttcttctgtaatttactgtttcttttcgtgttgttcctgcagGAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG