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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttatgaaaaatatcgtgggtgctcggctgcatctgccgcaattcttggtcttgagcactgtgtatacatgtatttttgtttctttattgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG

Basic information

species Zea mays
transcript GRMZM2G160996_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160996_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g02360.1 (Oryza sativa), 3'ss of exon 1
tcatttatgaaaaatatcgtg--ggtgctcggctgc----atctgccgcaattcttggtcttg-agcactgtgtatacatgtatttttgtttctttattgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG
      |  | || || | |    ||  ||  ||      || | || ||  | |   |   | |    || | |    |  |||| |   ||||| || || ||||||  ||| |||||| |||| ||||||||| |||| |||||||||||||||||||| |||||||||||| | ||||||||| | |||||||||||||||||
------aatagaattagccttctagtcttctactatggaaattttcctcatctttgaatgacgtaatgatgagaaaggcta-atttctcaatctttgtttctggcagTTGTCAAATTTGCCCGGGAAACAGGAGACCTCCAGACGCTTTCAGATGTTGATATCAAGATTATTGCTCTAGCTTACATGCTGGAAGCTGAGATCCATGG
















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|211459185|gb|FL298370.1|FL298370
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|89251870|gb|DY623656.1|DY623656
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|211459178|gb|FL298363.1|FL298363
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|211459181|gb|FL298366.1|FL298366
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|148959816|gb|EC905688.2|EC905688
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|26559222|gb|CA831457.1|CA831457
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|149015217|gb|EE045002.2|EE045002
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|22546382|gb|BU098693.1|BU098693
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|148957779|gb|EC903910.2|EC903910
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCCAAACGCCTTTCAGATGT
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCC-AAACGC-TTTCAGATGT
EST: gi|91867714|gb|EB399765.1|EB399765
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|211459175|gb|FL298360.1|FL298360
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|71320125|gb|DR796817.1|DR796817
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|211459186|gb|FL298371.1|FL298371
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGT-G
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|87157045|gb|DY401834.1|DY401834
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
EST: gi|211459183|gb|FL298368.1|FL298368
EST:     CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGATAAGAAAG                         TTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG
genomic: CCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTG

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: 46 (upstream exon), 47 (downstream exon)
Score: 97

GTGCTCGAGGAGGTCCGGGACGCAACCGCGCGGCGGCGCCTCGGGCTCCTCCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 39

GTGCTCGAGGAGGTCCGGGACGCAACCGCGCGGCGGCGCCTCGGGCTCCTCCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

GTGCTCGAGGAGGTCCGGGACGCAACCGCGCGGCGGCGCCTCGGGCTCCTCCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 46

GTGCTCGAGGAGGTCCGGGACGCAACCGCGCGGCGGCGCCTCGGGCTCCTCCCCGTTCCCGTTGAGACCGTTGAACCTGCGCCGGAGTTCGTTAAGAAAGgtcgctgctc ... ttgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttggtcttgagcactgtgtatacatgtatttttgtttctttattgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG
                               tttttgtttctttatt  CT-rich tract
                          atgtatttttgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttatgaaaaatatcgtgggtgctcggctgcatctgccgcaattcttggtcttgagcactgtgtatacatgtatttttgtttctttattgcttgcagTTACCAAGTTTGCCAGGGAGACAGGAGACATCCAAACGCTTTCAGATGTTGATATAAAGATTATTGCTTTGGCTTACATGTTAGAAGCTGAGATCCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - -aaaaata
- - - - - - - - - - gggtgct
- - - - - - - - - - - - - -cggctgc
- - - - - - - - - - - - - - - - - - ctgccgc
- - - - - - - - - - - - - - - - - - - - - - attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacatg