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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggcgtcggtttgaattctcgggccggtgcttcgatgactgtttcctcacgcttcgtttgtcggtgtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGTTTTTTTTTTCGACTG

Basic information

species Zea mays
transcript GRMZM2G110143_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 2
gtcaggcgtcggtttgaattctcgggccggt-gcttcgatgactgtttcctcacgcttcgtttgtcgg------tgtcctcgc-----agGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGTTTTTTTTTTCGACTG
|| ||| | || |||   |    |||  | | | |  | |   |||||  ||  | |   ||||          |||   |||     ||||| |||||||||||||| || ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||                    
gtgaggagccgctttttttgggtggggtgtttgttctgctcgttgttttgtctggatgtttttgctcaaaattttgttgccgctattaagGACTGGGGACTCGAGGGGATTCGCGTTCGTGCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG--------------------
















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|211438564|gb|FL360647.1|FL360647
EST:     CGAGCGCTGCGGGCAAGGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGNACTCGAGGGGGTTTTGCGTTCGTGCGG
genomic: CGAGCGCTGCGG-CAAGG-TCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGG-TTTTGCGTTCGTGCGG
EST: gi|211235451|gb|FL353173.1|FL353173
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|211008119|gb|FL365557.1|FL365557
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|149070638|gb|EE159049.2|EE159049
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|211161811|gb|FL316356.1|FL316356
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTAC
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTAC
EST: gi|149107883|gb|EE292243.2|EE292243
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
EST: gi|78105340|gb|DV523758.1|DV523758
EST:     TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAG                         GACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA
genomic: TTCGAGCGCTGCGGCAAGGTCGTCGACGTCTTCATCCCGAGGGACCGCAGgtcaggcgtc ... gtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggccggtgcttcgatgactgtttcctcacgcttcgtttgtcggtgtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGTTTTTTTTTTCGACTG
                       tcctcac  putative branch site (score: 2)
                                            tgtcctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggcgtcggtttgaattctcgggccggtgcttcgatgactgtttcctcacgcttcgtttgtcggtgtcctcgcagGACCGGGGACTCGAGGGGTTTTGCGTTCGTGCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGGTGGTTTTTTTTTTCGACTG

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