Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgggttcgctgctgtgtgaatccatgcgctctggtttcgagtcttcaaggtttgctgggtggaatttatgatctaagtctaacggtgtggttcttggtttttttttggggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG

Basic information

species Zea mays
transcript GRMZM2G050961_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050961_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g41710.1 (Oryza sativa), 3'ss of exon 1
gtgggtgggttcgctgctgtgtgaatccatgcgctctggtttcgagtcttcaaggtttgctgggtggaatttatgatctaagt-ctaacggtgtggttcttggtttttttttggggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
            |   | |  | |   |  | |    |  |||||||      ||||||  |||      || |||  |  || |||| |   |   |  ||||  | || | |  |   |||||||||||||||  ||||||||| |||||||| || || ||||| ||||||
------------gtaaccgcatta---cgggtggctcgagttcgagttccaggggtttgggggggtagggttctgacgtctgtgctaatgtgctatctggtggtggtgttgttgttgtc-cagGTGGCGCCGCAGTCCGACCGGGTGCTCGTCCGCCTCGAACAGATTCCTGAG
















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|13558469|gb|BG549825.1|BG549825
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|148943634|gb|EC888698.2|EC888698
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|211482968|gb|FK973427.1|FK973427
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|15198996|gb|BI423600.1|BI423600
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|13558001|gb|BG549357.1|BG549357
EST:     GACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: GACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|148943633|gb|EC888697.2|EC888697
EST:     CCGACGGG-TGGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCGACGGGCT-GGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|211485846|gb|FK973438.1|FK973438
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|29577011|gb|CB617123.1|CB617123
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|211061029|gb|FL204116.1|FL204116
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|29167933|gb|CB411193.1|CB411193
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|19058714|gb|BM737381.1|BM737381
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|29947167|gb|CB816515.1|CB816515
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|13382242|gb|BG458917.1|BG458917
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|211058063|gb|FL204109.1|FL204109
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|32849976|gb|CD989657.1|CD989657
EST:     ACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: ACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|13237244|gb|BG355258.1|BG355258
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|29544990|gb|CB605168.1|CB605168
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
EST: gi|26559456|gb|CA831691.1|CA831691
EST:     CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAG                         GTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
genomic: CCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 330

CTTCCTAGCCAGCAGCGGCAGCAGCCGCAGGCCGCTAGGCGCTGCCCACACCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 626

CTTCCTAGCCAGCAGCGGCAGCAGCCGCAGGCCGCTAGGCGCTGCCCACACCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

CTTCCTAGCCAGCAGCGGCAGCAGCCGCAGGCCGCTAGGCGCTGCCCACACCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

CTTCCTAGCCAGCAGCGGCAGCAGCCGCAGGCCGCTAGGCGCTGCCCACACCCGACGGGCTGGACTGCGCGTGGCCGCGCTTAAGTACGACCCTGCCAAGgtgggtgggt ... gggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttatgatctaagtctaacggtgtggttcttggtttttttttggggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG
              gtctaac  putative branch site (score: 325)
                                   ttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgggttcgctgctgtgtgaatccatgcgctctggtttcgagtcttcaaggtttgctgggtggaatttatgatctaagtctaacggtgtggttcttggtttttttttggggggggcagGTGGCGCCGCAGAACGACCGGGTTCTCGTCCGTCTTGAGCAGATCCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT