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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag

Basic information

species Zea mays
transcript GRMZM2G169694_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| |||||||||||| ||||||||||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||| || ||| | | || | || |||| ||| | || | | | | | || | | | | | | | || |||
GGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAAgtatgttctctcatctccatgtgcgcacatgggtggcatgtgtgttctca--ctaactgcttttatactagcaacaatgcagc-agaccaacagagaatt---gcc-------------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 4
-GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|| || ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || ||||||||||| | | ||||||||||||| || | | | ||| | | ||| | || || || | || | ||| | |||||| | || | | ||| ||||
GAGACACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATCGCTTATGATGTTGCAAgtatgctacttagggtgt---------ttcccttcacatattcctttctttttgc-tataaaatttaagttttctcaggga---atatctgtccaaaacatcactattt--ggac----------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || || ||||| ||||||| ||||||||||||| | | | | || | | | || | || | | | | | | | | | || | | || | | || || |||| | |
GGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAAgta--cgtcatttgggattcgctttcttttcac-----cttttactattgcccactatttgatgctatc--ttac-atggttttgtcttttaataaaagttaatctgatc---------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || |||||||||||||| | ||||||||||||| | || | | || || |||| | || || | | ||| | || | | | || | | || | ||| | ||| |||| ||
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgta---tgccattttg----acctactttcttttcaactattccct----------catgacaaattatattttcttgcaggtttttcatttcattataataatatattaatagt-ta-------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgta----atct---ccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || |||||||||||||| | ||||||||||||| || | || || || | ||| | || | | | || | | ||| || | | |||| || || ||| | | |
GGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatttagacctgctttctttcacctattccctccatgacgaattatattttcttgcagatttttcatttcaata--taataatatattaatagtta------------------------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| ||||| ||||||||||| || ||| | ||||||||||| || || ||||| || || ||||| ||||||| ||||||||||||| | | | | | | | | | || ||| | | | | | | | || || || | || || |||| | |
GGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAAgta--cgtcatttggggtttgctttcttctcac-----cttttactgttgcccactatttgatgctatc--ttacatggcttttgccttttaataaaagttaatctgat----------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G04340.1 (Glycine max), 5'ss of exon 4
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGT----CATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
||| || ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || |||||||| ||| | || ||||||||||||| || | | | || |||| | || | | | || | | | || || | || | |
GGACACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTACgtcatcgcatatgatgttgcaagtatgctatttagggtgtttcccttcac-ctat-----tcctttctttttgctgcttttgctttataattataattaagtgatg-----------------------------------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgta-----atctcc-----ctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttacta--ttttgttcttacctttttgtttcatgttgtag--
|||||| ||||| || || ||||||||||| ||||||| |||||||| || || || || |||||||| ||||| | ||||||||||||| | || | ||||||| ||||| || | | | || || || | | | | || ||| || ||| |||| ||| | || | | ||| || | | ||| || || | || ||
GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAAgtatgtgtaccttcactcgttctctcaaacacatgaatattttccca-tatctgagatcttggggatgtggttttcagtaatc-ttatgaatttatgcgtttcgatttcttctttatgttgatccattgtgcgttgtgaaactcgagatttattttgttttccactgacatatag

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgta--atctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
|||||| || || |||||||||||||||||| | ||||| ||||| ||||| || || || ||||| |||||||||| ||||||||||||| | ||| | | | | | |||| | | | | | | | || | | || | | || | | || | | |
GGATACAGCCGGGCAGGAAAGATTCAGGAGTCTCATTCCGAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatcctttatttctctgccatctttcttt---tttggcttcttgaatagtttttgcattgtagatgattattct-aattgttgcctgatgggcatgtt-----------------------------------------------------------

upper sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 3
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatc-tccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag
||||||||| || |||||||| ||||||||| | || ||||| || ||||| ||||| || ||||| |||||||||| ||||||||||||| | | || || || | |||| | | |||| || | || | || || | | | | | ||||| ||
GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgcatttttcgcttttattttc-cattatggaaaaatgtttctcatct-attcatgtctttttctttctctcttttgtttccctcccttttgggtactt------------------------------------------------------------

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|211199864|gb|FK959366.1|FK959366
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|71333156|gb|DR803613.1|DR803613
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|32919616|gb|CF024428.1|CF024428
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|148970042|gb|EE020962.2|EE020962
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|33093555|gb|CF053549.1|CF053549
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|37397830|gb|CF636223.1|CF636223
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|149085277|gb|EE174782.2|EE174782
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|89251359|gb|DY623145.1|DY623145
EST:     CAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCCTA-GTGGATAGAGGAAGTTCGCACT
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATC-TAAGTGGATAGAGGAAGTTCGCACT
EST: gi|71333158|gb|DR803614.1|DR803614
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|56462112|gb|CK986410.1|CK986410
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|213167949|gb|FM194944.1|FM194944
EST:     ATTGTATTCTATGTTGCAA                         GCAGGCAGTCCTTCTT-AATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: ATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|148960910|gb|EE011595.2|EE011595
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|213169997|gb|FM189153.1|FM189153
EST:     NAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|87152147|gb|DY396936.1|DY396936
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|32870836|gb|CF010518.1|CF010518
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
EST: gi|149085276|gb|EE174781.2|EE174781
EST:     AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG
genomic: AAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTG

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: 201

GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccc ... catgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT