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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaacttattgtgtaattggtaggattaggcttacggaggaagtacgtggggtaggttttagatctagtaccaggaccccgacgcttgggcaccg...

Basic information

species Zea mays
transcript GRMZM2G423027_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423027_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g44280.2 (Oryza sativa), 5'ss of exon 2
TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaacttattgtgtaattggtaggattaggcttacggaggaagtacgtggggtaggttttagatctagtaccaggaccccgacgcttgggcaccg-----
     ||||| |||||||| || || || |||||||| ||  ||||| ||||||| ||||||||| | ||||||||||| ||||| ||||| |||||||| ||||||  |   |     |  |  |  | || |    |       |     |    || | |    |  ||  |     |    |   | |    || |     
-----TACAACGCCACCATTTCTGCGCCTCACATGCACGCCTCTTGCTTGGAGCTCCTGGAGAAGCACCTTCAGCCTGGCATGCGTGCTCTGGATGTTGGATCAGgtctcccgtatctcatatattcagtttcgctcaatcacttcaacgttttatctatgctcctaaaatatcatttcaattatgtatcatcacaacagaaaca

upper sequence: GRMZM2G423027_T06 (Zea mays), 5'ss of exon 2
lower sequence: EFJ13692 (Selaginella moellendorffii), 5'ss of exon 1
TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaacttattgtgtaattggtaggattaggcttacggaggaagtacgtggggtaggttttagatctagtaccaggaccccgacgcttgggcaccg
     | |||||||||||| || || |||||||||||||   | ||||||||||| ||  | ||| |||| ||||| |||||||  |||||||| ||||| || ||||    |    |  |||  |    ||   |||   |        | |  |  |  ||||  ||||  |    | |                   
-----TTCAATGCCACCATCTCGGCTCCACACATGCATGGCTCGTGCCTGGAGCTTCTCAACAAGCATCTCCAGCCGGGAATGCACGCTCTCGACGTTGGCTCCGgtatgaaa----gagatttctctcttttttcttcttggtttgcatcctctgaaattttttctatcttctctttgcag------------------

upper sequence: GRMZM2G423027_T06 (Zea mays), 5'ss of exon 2
lower sequence: EFJ28990 (Selaginella moellendorffii), 5'ss of exon 2
TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaacttattgtgtaattggtaggattaggcttacggaggaagtacgtggggtaggttttagatctagtaccaggaccccgacgcttgggcaccg
     | |||||||||||| || || |||||||||||||   | ||||||||||| ||  | ||| |||| ||||| |||||||  |||||||| ||||| || ||||   |       | ||     | ||   |||   |        | |  |  |  ||||  |||                              
-----TTCAATGCCACCATCTCGGCTCCACACATGCATGGCTCGTGCCTGGAGCTTCTCAACAAGCATCTCCAGCCGGGAATGCACGCTCTCGACGTTGGCTCCGgta---tgaaagaaatttctctcgttttttcttcttggtttgcatcctctgaaaaattttctatcag----------------------------

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|101382804|gb|EB813457.1|EB813457
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|211322149|gb|FL087639.1|FL087639
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTG
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTG
EST: gi|74240646|gb|DT648560.1|DT648560
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
EST: gi|211178420|gb|FL087636.1|FL087636
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
EST: gi|211178419|gb|FL087635.1|FL087635
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
EST: gi|71764019|gb|DR961956.1|DR961956
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
EST: gi|211178414|gb|FL087630.1|FL087630
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGGACCAG
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGG-ACCAG
EST: gi|89761173|gb|DY689295.1|DY689295
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
EST: gi|76293016|gb|DV032584.1|DV032584
EST:     GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGG                         GTCAGGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA
genomic: GAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagG-CA--C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 9 (downstream exon)
Score: 3

TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaac ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGGTACAATGCCACCATATCAGCACCACACATGCATGCGGCTTGCCTGGAGCTACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGgtcaggtaacttattgtgtaattggtaggattaggcttacggaggaagtacgtggggtaggttttagatctagtaccaggaccccgacgcttgggcaccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccgac