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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacaattcgattcgaggcaccttcttttcggctcgttgccttgaagccggcctgacgctgttgttttggattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGCGCCGAAGAGCCCGATAG

Basic information

species Zea mays
transcript GRMZM5G815165_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G815165_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g53800.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gtatgtacaattcgattcgaggcaccttcttttcggctcgttgccttgaagccggcctgacgctg--ttgttttggattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGCGCCGAAGAGCCCGATAG
                                                |    ||   || |  |      | |   || |||   | ||| | ||  |  | |  ||  || || |||| |||||||||||||||| ||||||| || || ||||||||||||||  | ||||| || || || ||||| || ||
gtaagcaacattcgacgagcctttctgtctcgatcactgaaatccgcatgttgtttttttagtagtcatggcctcatgggtcgcaac-ttgcaaccaacgagccaatggtttcttgtggagtttgcagGGGAATGATACGATGGCCACCATCGAGAATGTCTTCGCGGTGATCGAAGGTGCAGAGGAGCCGGACAG
















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|12046047|gb|BF728186.1|BF728186
EST:     CCG-TTACCGCCTCGGGCCAGGGCCGGCAG-TTTGAACCTGACATATCTT                         GGGAATGATTCGATGGCAACGATTGAGAATGNNNNNNNNATTATCGAGGGC
genomic: CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTTgtatgtacaa ... gattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
EST: gi|6827070|gb|AW330713.1|AW330713
EST:     CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTT                         GGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
genomic: CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTTgtatgtacaa ... gattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
EST: gi|7844379|gb|AW787601.1|AW787601
EST:     CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTT                         GGGAATGATTCGATGG
genomic: CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTTgtatgtacaa ... gattttgcagGGGAATGATTCGATGG
EST: gi|78180604|gb|DV550932.1|DV550932
EST:     CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTT                         GGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
genomic: CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTTgtatgtacaa ... gattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
EST: gi|149019466|gb|EE154376.2|EE154376
EST:     CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTT                         GGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC
genomic: CCGTTTACCGCCTCGGGCCAGGGCCGGCAGTTTTGAACCTGACATATCTTgtatgtacaa ... gattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcggctcgttgccttgaagccggcctgacgctgttgttttggattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGCGCCGAAGAGCCCGATAG
                          gcctgac  putative branch site (score: 3)
                                     ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacaattcgattcgaggcaccttcttttcggctcgttgccttgaagccggcctgacgctgttgttttggattttgcagGGGAATGATTCGATGGCAACGATTGAGAATGTCTTCGCCATTATCGAGGGCGCCGAAGAGCCCGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA