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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacattctgctatcttgagcaagttctaggaaaacaaattacatgatgctacttatgcagttacactctattattttatggttatggccacacttcaattgtttgggtaaatcctacctgttcctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATCCATTAGATGTGATATTTGAG

Basic information

species Zea mays
transcript GRMZM2G042074_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 12
gttagtacattct-gctatcttgagcaagttctaggaaaacaaattacatgatgctacttatgcagttacactctattattttatggttatggccacacttcaattgtttg------ggtaaa----tcctacctgttcctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATCCATTAGATGTGATATTTGAG
    ||   | || ||| | ||||  ||||| | | | |||       |   | |   || | |   | |  | ||   | ||||| |||  || || ||||||||| ||       | ||      || |||||  |  | |||||||||||||||||||||||||   ||||||||||||  ||| ||| ||||| ||||| ||||| ||  || ||
----gtgattcctcgctctgttga-taagtttt-gaagaactgccagtaaattaca--ttgttctccttctttttaac-tattatgtttactgctacccttcaattgattcatgcttgatatgactttcttacctactattctttcagTTGATTCTTTATGCCTCGATGCTCCAGGATGGGAAATTAGATCGAAACACCCATTTGATGTCATTATTCAG
















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|67033220|gb|CO461969.1|CO461969
EST:     AACGATCTTGTACCGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAG                         TTGATTCTTTATGCCTCTACATTCCAGGATGGGAGGTTACATCCAAACATC
genomic: AACGATCTTGGA-GGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAGgttagtacat ... cctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATC
EST: gi|6637081|gb|AW261353.1|AW261353
EST:     AAACGATCTTGGAGGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAG                         TTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATC
genomic: AAACGATCTTGGAGGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAGgttagtacat ... cctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATC
EST: gi|61119040|gb|DN560001.1|DN560001
EST:     AAACGATCTTGGAGGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAG                         TTGATTCTTTATGC
genomic: AAACGATCTTGGAGGCAATTGCGAAGTTGACCATGGTTTGTTTTGTCCAGgttagtacat ... cctgtttcagTTGATTCTTTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttatggccacacttcaattgtttgggtaaatcctacctgttcctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATCCATTAGATGTGATATTTGAG
                                  tcctacctgttcct  CT-rich tract
                   aattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacattctgctatcttgagcaagttctaggaaaacaaattacatgatgctacttatgcagttacactctattattttatggttatggccacacttcaattgtttgggtaaatcctacctgttcctgtttcagTTGATTCTTTATGCCTCGACATTCCAGGATGGGAGGTTACATCCAAACATCCATTAGATGTGATATTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG