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

gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG

Basic information

species Zea mays
transcript GRMZM2G110328_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 5
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgat-atcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                                            ||  |  |  ||||    |     | | ||  | |   |   | || | ||| |       ||||||  |  |  |   |||| ||| |     |       | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||| | ||| ||||||| || | || |
-----------------------------------------------------------atgcataatcccctattgcatcttgtgtatgcataatcct---ccgatatacattt--cgatgatgctaaaggactaaattcatctgagcttatgca-----ttgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAGGCTGAGGTAACCAAGTCCCAGAAGTCGCAGTCGAAGGGTGCCGCCCCG

upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgat-atcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                                            ||  |  |  ||||    |     | | ||  | |   |   | || | ||| |       ||||||  |  |  |   |||| ||| |     |       | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| |||                                                
-----------------------------------------------------------atgcataatcccctattgcatcttgtgtatgcataatcct---ccgatatacattt--cgatgatgctaaaggactaaattcatctgagcttatgca-----ttgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------

upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G37370.1 (Glycine max), 3'ss of exon 4
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGAC---CAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                                             || | |     || |      ||  | | | |    ||| |  |    |   |  | |    | |||  || ||   | ||  |||       ||       |||||||| || |||||| | |||||||| || ||||||||||||||||| || || || || ||  |   |||||| || || |||     ||| ||    ||    
------------------------------------------------------------cgtatat-attttaccttgtgtaaaattttatt--tgtttcagcgctttatttttaacagctctacttatta-catatttatcggaatctatgatgtgg----tgcagTGAAATTAAGGAGAGGATCAAGAAAACAAAGGATGAGAAGAAGGCTAAGAAAGCAGAAGTTGCTTCCAAGTCGCAAAAAGCAGGAGGGAAAGGCAATGTT---

upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 4
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaacca-acaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGAC---CAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                                            | | | ||    ||| ||   ||||| |   | |    |||  ||||  |  | |   || |  ||  | | || | | | || |||    |   ||       |||||||| || |||||| | |||||||| || ||||||||||||||||| || || || || || ||   |||||| || || |||     ||| ||          
-----------------------------------------------------------gtattttttactttaatcatgtaaaatatt--atttctgttt--cagagccttacttttta-atgtggattacat-atgtttatctgagtctctgatgtgg----tgcagTGAAATTAAGGAGAGGATCAAGAAAACAAAGGATGAGAAGAAGGCTAAGAAAGCAGAAGTTACAGCCAAGTCACAAAAAGCAGGAGGGAAAGGCATTTCT---

upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaaca-caatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAG---GTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                                                                    |  | ||  |||| | |  | | ||| ||||   |         ||| ||  |  | |||  ||      ||||    | |||||||||||||||||| | ||||||||||||||||| ||||||||||| || ||||  |||   |   | |||   |||||| ||||   |||||||    ||   
--------------------------------------------------------------------------gtttgtttctttcccgaa-gacagtcactatatacatcaatttttttttgaaactgaaatgtgattgattcaaagctaatctgatgattatgcagTGAGATCAAGGAGAGAATCAAGAAGACCAAGGACGAGAAGAAGGCAAAGAAGGTCGAGTATGCATCAAAGCAACAGAAGTCACAAGTGAAGGGAAATATC---

upper sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGA---CCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                        |||  ||| |       |||| |||        ||    |    ||||  |   || | |       ||  |  ||     ||   ||   ||    || | ||| |      |||  ||||  ||||||| || || ||| | |||||||| ||||||||||| ||||| || || ||||||||||| |   ||||| | |||||  | ||||  ||||| | |      
----------------------------------------gtgggtatcattccttgaactttcta-------aatttgctgggtctcccaaatacctattgttagcacttagcagtgggcgaaattttccatt---ctgaattgcat-tattctgtaacct--gcagTGAAATTAAAGAGAGGATCAAGAAAACCAAGGATGAAAAGAAAGCCAAGAAGGCTGAGGTAATGGCCAAGACGCAGAAAACTCAGAGCAAGGGTGTGCCT---

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|8103338|gb|AW927981.1|AW927981
EST:     CTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: CTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|76281134|gb|DV020702.1|DV020702
EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTTTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|31357325|gb|CD441682.1|CD441682
EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         CGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|12046861|gb|BF728987.1|BF728987
EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|71419243|gb|DR804694.1|DR804694
EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|76281135|gb|DV020703.1|DV020703
EST:     AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: AGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
EST: gi|18181413|gb|BM382623.1|BM382623
EST:     GCGATGCTGCTAGAGAAGCTGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA
genomic: GCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAA

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: 1043

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 918

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 932

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 557

CATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGAGGGCTGAGAAGCCCGAGGTCCGCGATGCTGCTAGAGAAGCTGCTCTTCGgtatgcttgt ... acctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatacagatgcttgatatcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
                                      cactgac  putative branch site (score: 557)
                                            caccttt  CT-rich tract
             ttgatat  TA-rich tract