Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG

Basic information

species Zea mays
transcript GRMZM2G123140_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 11
aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaa----cagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG
  || |  | | |  |  |  |   | |    |     ||   ||| |   | | |||     || |  |  | ||    |   |||| |||||  |    ||||||||||||||||| || ||||| ||||||||| ||||||||||||||||||||||||| || || |||||||| |||||||| ||||| ||||||||||
--ataa--tgagagttgcttactttacttttttccctctgctgattgaaactagatatataacaagagctgacctttttccaattgataaaaactgatgtccagGCTGCAAGCAACTCGTCACAGAATGTGGAGCTCCTGCTGCAGGAGAGCAGCACCCACCCTGATGGTGGGAGCCTGGTGGTGTTCGCGACGGTGGACGTGG

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 10
aaattactttatacataatccc-caaaatacagtttacttgagcattaagc--attgttatg-actgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
|||||     ||   ||||        | |  || || ||       |||   |  ||| |  | |  |||| ||   ||     || | |   | |    ||||  || |||||||||||||||||||| ||||| |||||||| ||||   ||||| |||   |    || ||| | || ||||   | ||| | |||||||   
aaattgtgaaatttttaatttgatgtgaaatggtctaattagaatgcaagtgaaaggttctctattccaaaccttaggtta----ttgttacatatatatgcagGTAGCGAGCAACTCATCCCAGAACGTAGAGCTAATGCTGCAAGAGAATTGCACCGACC---AATCTGGAAGCATAGTAGTGTACACAACCATCGACGTGGATT

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 10
--aaattactttatacataatccccaaaatacagtttacttgagcattaagcattg--ttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
   | ||  |||||      |      ||   |  ||| |  |     |   |  |  ||   | |  |||| ||   ||     |||  |   | |    ||||  ||||||||||||||||||||||| ||||| |||||||| |||||  ||||| |||   |    || ||||| || ||||   | ||| | |||||||   
tagagtttttttatttgatgtgaagtgaaatgatcttattaaaatgcaagtgaaaggttttctattctaaaccttaggtta----ttcctacatatatatgcagGTAGCAAGCAACTCATCCCAGAACGTAGAGCTAATGCTGCAAGAGAGTTGCACCGACC---AATCTGGAAGCCTAGTAGTGTACACAACCATCGACGTGGATG

upper sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 10
------aaattactttatacataatccccaaaatacagtttacttgagcattaagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG---
      |||| | |    |   ||||  |   |    ||   | | |   || | |    |||  | ||   |  ||  |  |   ||| | ||| |  |    |||  || ||||| ||||| |||||||| |||||||||||||| |||||| ||||| |||   |   ||| |||| |||||| |   | ||| | |||||||   
gagatgaaataagtgctgaaccaatcttctttaggaggtgctcatcaattttcatctaatttaaaagtgtgtaaatt--agagacccttttcatgcatgc----agGTGGCCAGCAATTCATCACAGAACGTAGAGCTCATGCTGCAAGAGAGCTGCACCGACC---AGTCCGGCAGCCACGTGGTTTACACCACCATTGACGTGGATG

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|31910760|gb|CD651585.1|CD651585
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|71321764|gb|DR797569.1|DR797569
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|22819056|gb|BU499146.1|BU499146
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|5555586|gb|AI881537.1|AI881537
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|71329968|gb|DR801717.1|DR801717
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|87157207|gb|DY401996.1|DY401996
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|30306491|gb|CD001164.1|CD001164
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|26559801|gb|CA832036.1|CA832036
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
EST: gi|31558675|gb|CD527887.1|CD527887
EST:     TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT                         GCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC
genomic: TTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGC

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 63

CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 6

CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 8

CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAATgtgagtacat ... aaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcattgttatgactgaaaacttttcattgcatcttctgatgaaaaccaacagGCTGCAAGCAACTCATCCCAGAACGTGGAGCTCATGCTGCAGGAGAGCAGCACCCACCCCGACGGCGGGAGCCTCGTGGTGTTTGCGACCGTGGACGTGG
                                    ttctgat  putative branch site (score: 8)
                  aaaactttt  TA-rich tract