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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatgttactccatgtacttggggatatatatcaatatcttgagttgtagactgcagtgtgttatctatttgatttttgatgtttcagttttatg...

Basic information

species Zea mays
transcript GRMZM2G174107_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g25624.3 (Oryza sativa), 5'ss of exon 7
GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatgt-tact-ccatgtacttggggatatatatcaatatcttgagttgtagactgcagtgtgttatctatttgatttttgatgtttcagttttatg
|||||||||||||| || || |||||||||| | |  | |||| ||| |||||||| || |||||||||||||||||||  | ||  | | |  |   |  |    ||  | || || |||||  ||  |  |   ||| | | | || ||           |  |  || 
GGTCTGAATGTAAAACAGGTGCTTACAAGGTCTTTACTTGCTGCACTTTGTTTCCACGCGTACCAACAGgttagtcatgcatgctgtcgttttttcatgtttggtcatatacatgtttagttg-ggatagttgatagttctgtttatggttcaaatgccagaaagtgcat-
















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|32842413|gb|CD982094.1|CD982094
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|60351427|gb|DN218400.1|DN218400
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|60354172|gb|DN221145.1|DN221145
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|16378321|gb|BI992391.1|BI992391
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|16377738|gb|BI992093.1|BI992093
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|13177801|gb|BG349164.1|BG349164
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|13178610|gb|BG349868.1|BG349868
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|32941693|gb|CF046512.1|CF046512
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|13150806|gb|BG321128.1|BG321128
EST:     CCTTACAAGGTGTCTTTTCGCTGGACTGTGTTRCCATGCATACCAKACAG                         GTGTCTTACATGATTTTGGCGATGGTGGTCTCCTGTCACTCATTCTGTGG
genomic: CCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCA-ACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGT-GTCTCCTGTCACTCATTCTGTGG
EST: gi|32842414|gb|CD982095.1|CD982095
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|32940452|gb|CF045271.1|CF045271
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|148937400|gb|EC881580.2|EC881580
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|5688709|gb|AI941724.1|AI941724
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|211517932|gb|FL479804.1|FL479804
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|7227535|gb|AW566176.1|AW566176
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|148940598|gb|EC885404.2|EC885404
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|83279370|gb|DV943378.1|DV943378
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|15427333|gb|BI543155.1|BI543155
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|56462047|gb|CK986345.1|CK986345
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|24934366|gb|CA452584.1|CA452584
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|211376284|gb|FL144046.1|FL144046
EST:     GGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: GGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|13126160|gb|BG316730.1|BG316730
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
EST: gi|4624425|gb|AI615258.1|AI615258
EST:     TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAG                         GTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC
genomic: TCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 41

GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGCAACTGTGTTAAACGTGTTGTGGTCATTGTAACATCAGTGCTGTTCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 542

GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGCAACTGTGTTAAACGTGTTGTGGTCATTGTAACATCAGTGCTGTTCTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 16

GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGCAACTGTGTTAAACGTGTTGTGGTCATTGTAACATCAGTGCTGTTCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatg ... ttgtttgaagGTGTCTTACATGATTTTGGCGATGGTGTCTCCTGTCACTCATTCTGTGGGCAACTGTGTTAAACGTGTTGTGGTCATTGTAACATCAGTGCTGTTCTTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCTGAATGTAAACCAAGTCCTTACAAGGTGTCTTTTCGCTGGACTGTGTTTCCATGCATACCAACAGgttagtcatgttactccatgtacttggggatatatatcaatatcttgagttgtagactgcagtgtgttatctatttgatttttgatgtttcagttttatg

- - - - - - - - - - - - - - - - - - -  GCTGGA