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

gtcagcccccgtccctgactttgacaacctttacttccaaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG

Basic information

species Zea mays
transcript GRMZM2G067985_T09
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 2
--------------------gtcagcccccgtccctgactttgacaacctttacttccaaatatgccacta-attatgtct-gtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                     | |  |        ||   |  |   | | | || |  |||||  || || ||||  | |  || | ||||||||||| ||||| ||||||||||||||||| || |||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| |||||||| |
gtctgattttctttttcttttttactcttacgtaatgtaatgtatgtcgtctcctgctgaatattacattacattacatttcatcatgtagGCTGGTTTCGCTGGGGATGATGCACCAAGGGCCGTGTTCCCTAGTATTGTTGGCCGTCCTCGCCACACCGGTGTTATGGTAGGAATGGGGCAGAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 2
----------------------------gtcagcccccgtccctgactttgacaacctttacttccaaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                            ||       | ||  | | | |      | |||       || |    |||      ||||| |   |||| || |||||||| |||||||| || ||||| || || || || ||||||||||| ||||| || |||||||| ||||| |||||||| || ||||| |
gttagtactttgcagtttcttctgttatgtgtaattgcatctattagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtac-agGCAGGATTTGCTGGTGATGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGCCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 2
-------------------gtcagcccccgtccctgactttgacaacctttacttc-caaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                    |        |    ||  | ||  |  ||| | |||  || |     | | ||| |   | |     |||| || |||||||| || ||||| || ||||| || || || || ||||||||||| ||||| || |||||||| ||||| |||||||| || ||||| |
gttagtacttcgtggatttttgttttgttgcatgtgcatatgcaagtcttgagttcataagtgaataatttattttaa-tatggaacagGCAGGATTTGCTGGTGACGATGCTCCTAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------gtcagcccccgtccctgactttgac-aacctttacttccaaatatgccactaat---tatgtctgtct-------tttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                               |    |      | |||   |||   |   || | |   |||||||  | | ||   ||| | | |||       |  ||||||||||||| || |||||||| || ||||| || ||||| |||||| ||||  | || ||||| |||||||| ||||| |||||||| |||||||| |
gttagaagatgttttgccaattgatgagtgtttcttgtgccattgaagaagactgttcactctgtgcttgcttagtattcattgttaaatatgatattgatatatatatttttctcgatgtttgcagGCTGGTTTTGCAGGTGATGATGCTCCTAGGGCCGTGTTCCCCAGCATTATTGGGAGACCACGCCATACTGGTGTAATGGTTGGGATGGGTCAGAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 1
-----------------------gtcagcccccgtccctgac--tttgacaacctttacttc-caaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                        |     |  || | ||    | ||  | |||| | |||  || |    |  | ||| |   | |     ||||||| |||||||| |||||||| || ||||| || || || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || ||||| |
gttagtacttagcggctttgttttttgtttcatgtgcttgtgcatctgctagccttgagttcataactgaatctttgattttaa-tatggaacagGCTGGATTTGCTGGTGATGATGCTCCCAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACACACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------gtcagcccccgtccctgactttgacaacctttact-tccaaatatg---ccactaattatg---tctgtctttta---gGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                  | ||   | ||   ||  | | ||   ||||  | | ||  | |    | ||| || |||   | ||| | |||   ||||||||||||||| |||||||| || || || || ||||| || |||||||| |||||| | ||||||||||||||||| || ||||| ||||| || |
gtgagttagactgtttatttagatactgta--tggttctaaccttctttgttgtacatgtgtaagactactgatcatgatttttgtatattaacagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtcagcccccgtccctgactttgacaacctttacttccaaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                   ||  |      |  |||    | | |  ||  | ||  | |       |   |||||  |    |  ||||||| ||||| || |||||||| || ||||| || || ||||| ||||| || || ||  | ||||||||||||||||| |||||||| || || || |
gtctgttgtttctttcttgcttgatatgcagatttgtt-gtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcagGCTGGATTTGCGGGTGATGATGCTCCCAGGGCAGTGTTTCCTAGTATTGTGGGTCGGCCAAGGCACACTGGTGTCATGGTTGGGATGGGTCAAAAAGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtcagcccccgtccctgactttgacaacctttacttccaaatat-gccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                  |  ||   |     | |  ||    |  |||  || || | ||   | ||  | |    |||     ||||||| |||||||| |||||||| || ||||| || ||||| || ||||||||||| ||||| ||||| ||||||||||| |||||||| || ||||| |
attaaactgattctgtttgctgtggcgaggtgaatttgcattcagtgattatctttgttagttttgttttcacacattaacgctgctcaaaaatgtgc---agGCTGGATTTGCTGGTGATGATGCTCCGAGGGCTGTGTTCCCCAGTATTGTTGGCCGACCTCGACACACAGGTGTCATGGTTGGGATGGGCCAAAAGGATG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S381_21V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------gtcagcccccgtccctgactttgacaacctttacttccaaatatg---ccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                             | |   |    |   |  || | |  |  ||  |    || ||    |||  |||  ||  |||  |  |||| ||||| || || || ||||| ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
ctgcattcttagatttgtagtttgctaccttaatgcagtccttcgcgttaggcgtcagttgttgtggaagattgatccaaaaatggtgcatgtaatgcagGCCGGTTTCGCGGGAGACGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtcagcccccgtccct-gact--ttgacaacctttacttccaaatatgccactaattatgtctgtct---tttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                         | ||| |   |    | ||||  || |  | |  | ||  | ||  ||    ||||| ||      |      |||||||||| ||||| || ||||| ||  | || |||||||| ||||||||||| || ||  | |||||||| || ||||| || ||||||||||||||||
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
-------------------------------gtcagcccccgtccctgactttgacaacctttacttccaaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                |||   |   |  |||   || ||| |  ||    |   ||  |  |  |  |  |  | |  |  |||||||||| ||||| ||||| || ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
aaccttaacttgcgtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------gtcagcccccgtccctg--actttgacaacctttactt--ccaaatatgccactaat-tatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                                                                                              |||  |  |    | ||  |  |     | |   ||    || || |||    || | |  |  | |  |  |||||||||| ||||| ||||| || ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
gtatgatattaactgttttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtcagcccccgtccc-tgactttgacaacctttacttc--caaatatgccactaattatgtctgtct---tttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                         |  |   |   ||   ||||||         |  |     | ||   |    ||||| ||      |      |||||||||| ||||| || ||||| ||  | || |||||||| ||||||||||| || ||  | |||||||| || ||||| || ||||||||||||||||
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------gtcagcccccgtccctg--actttgacaacctttactt--ccaaatatgccactaat-tatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                          |||  |  |    | ||  |  |     | |   ||    || || |||    || | |  |  | |  |  |||||||||| ||||| ||||| || ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
lower sequence: PP1S381_18V6.2 (Physcomitrella patens), 3'ss of exon 2
-------------------gtcagcccccgtccctgactttgac--aacctttactt---ccaa-----atatgccactaatt--atgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                     |  |  | ||  ||   |        |||| |  ||   ||||     || |   | ||||    ||  |||  |  |||| ||||| || || |||||||| ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
gtagtatcaaatctccacaaccgtcttctgtgtctaggtcatgttggacctgtgtttaggccaatcaacatgtaggagtaatatggtgcatgtaatgcagGCCGGTTTCGCGGGAGATGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

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|5928698|gb|AW055915.1|AW055915
EST:     GAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG                         GCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
EST: gi|22543167|gb|BU093605.1|BU093605
EST:     GTGAGGACATCCAGCCTCTTG-CTGCGACAATGGCACTGGAATGGTCAAG                         GCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT

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: 49 (upstream exon), 49 (downstream exon)
Score: 839

AAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 781

AAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

AAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 725

AAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAGgtcagccccc ... tgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactttgacaacctttacttccaaatatgccactaattatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG
                                cactaat  putative branch site (score: 725)
                                           tctgtctttt  putative PPT
                                 actaattat  TA-rich tract