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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag

Basic information

species Zea mays
transcript GRMZM2G089630_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcga--tattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
| |||| || || ||||| || ||||||| ||||||||| ||| | || ||||||||||||||||| || |||||||||||||||||||||||||||||||||   | || || ||  |    |||||||   | | |  ||||  |      ||||| |   |   | || ||||| || |||
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtt-tcatgcctctt-cag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
  ||||  | || |||||| ||||||| | ||||||||| ||||| || ||||||||||||||||| || |||||||||||||||||||||||||| |||||| ||| || ||||  |   ||  ||    | | |  |||||  |    |||||| |   ||    || ||||||||||||
CTTACCAGTGCCAGAACTAATAAAATTTGTCTTTTTTGCAAACCTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTACCAGgtgaagaaagtaactaagtcctttaatgttcacttttagaattggatgcatatactaat-ttgctcctcatgcctttttcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G27820.1 (Glycine max), 5'ss of exon 2
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagtatat-cggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
| |||| || || || ||  ||||||| |   |  |||| ||| | ||||||||||| |||||||| ||  | ||||||||||| |||||||||||||| ||| ||   |      |  ||| ||||  ||  || |   | |    |   |   | |   |  || | | ||| ||  |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCGTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtg-agttgggctgagctttat-ctattggttcattcactaatgccttcagaagttaatattcactttttagccattgacag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G39590.1 (Glycine max), 5'ss of exon 2
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataag----tatatcggaattaaacttgtatactgacgc-tgtctgtcttgcctttttcag----------------
||| ||  || ||||  || | ||||| | ||| ||||| ||  | || ||||||||||||||||| || || ||||||||||||||||| |||||||||||      |     ||   ||  ||||||     |  | ||   ||| | |    ||  ||    | | | |  |   | || |                  
TCTTCCAGTATCTGATATAATCAAATTTGTCTTATTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataacattttgaaccgtctttataataaactaaagataaatatttataataattcttccttgaaattaaattgtcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G08700.1 (Glycine max), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
| |||| || || || ||  ||||||| |   | ||||| ||| | ||||||||||| |||||||| ||  | ||||||||||| |||||||||||||| ||| ||   |      |  ||| ||||  ||  ||          |||    | | |   |  || | | ||| ||  |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCTTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtg-agttgggctgagctttat-ctattggttaattcattaatgccttcagaagttatattcactttttagccattgacag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G15250.1 (Glycine max), 5'ss of exon 2
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatatt---ctataagtatatcggaattaaacttgtatactgac-------gctgtctgtcttgcctttttcag------------------
 || || |||||||| ||  | ||||| | ||| ||||| ||  | |||||||| || |||||||| || ||||||||||||||||| || |||||||||||    ||   |  ||   | ||   || | |   ||||    || |||      | ||||       | | | | |  ||  |  |||                    
CCTTCCCTTACCTGATCTTATCAAATTTGTCTTATTTGCAAATTTCTCTATTGTCGGCATGAATGTGAGTTTGATGTGGAACTCTGTCGGTTTCTATCAGgtaacaactatattttttttttttatctttgaaagtatcaagttttaacactgccagtgacaaagataggtatttatactgtttccttcctttgaaatgaaaacttcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G15280.1 (Glycine max), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagtatatcggaa-----ttaaacttgtatactgacgctgtctgtcttgcctttttcag----------------
||| || ||| ||||  || | ||||| | ||| ||||| ||  | || ||||||||||||||||| || || ||||||||||||||||| |||||||||||      |     ||   ||  ||||||  || | | |      ||| | |    |   ||   | | | |  |   | || |                  
TCTTCCATTATCTGATATAATCAAATTTGTCTTGTTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataa-cattttgaaccctctttatagtaaactctagataatatttataataattattccttgaaataaaattgtcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G36620.1 (Glycine max), 5'ss of exon 2
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtg---cagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
| |||| ||||| || ||  ||||||| |  || ||||| ||| | || |||||||| |||||||| ||  | ||||||||||| |||||||||||||| |||      |  |||  |||  ||||     |   |  |   | |  | |   |   | |   | |||   |  || ||  |||
TTTACCCTTACCAGAGCTTCTAAAATTTGTTTTCTTTGCTAACTTCTCCATTGTTGGAATGAATGTCAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgtattgaattttcactattggtccaaggt-ccattaatgcattcagaagttaa-attttcttcttaaccattggcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatattctataagtatatcggaattaaacttgtatactgacgctgt--ctgtcttgcctttttcag----
||| |||||  | || ||  | | |||     | ||||| ||  | || |||||||| |||||||| ||  | ||||||||||||||||| || ||||||||      ||| |         ||| ||| | |   | ||  |||  | | | ||||   | |   |||| ||  |||    |    
TCTTCCGTTTACGGAGCTTTTGAGATTTATTCTGTTTGCTAATTTCTCCATTGTTGGAATGAATGTCAGTCTTATGTGGAACTCTGTTGGTTTTTATCAGgtat---tagacatcatctagctctgtaattgt---gaaaagaaatgtat-tgctgattttatgattgtcctgtttttgcttgtcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcg-atattctataa-gtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
||| || ||  | || ||  | || ||     | ||||| ||  | || |||||||| |||||||| ||  | ||||||||||||||||| || ||||||||  |        |||    | || | ||| || | | |   ||     |    | ||  |   ||| | ||    ||  |||
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtgttatgtaacgtttcttgttgttggttct----aatggtgtcttctcttttatgcttaacag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 5'ss of exon 2
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcgatat-tctataagtatatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag
||| ||  | || || ||  | ||||| |  || ||||||||| | ||||||||||| |||||||| || || ||||||||||| || || |||||||||||  |  | ||    ||  | | | ||    || ||   | |  ||    |  |         ||| |  |     | ||||
TCTCCCCCTTCCAGAGCTTCTGAAATTTGTATTATTTGCGAACTTCTCTATTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAGgtatattctgattgctctgtgtgtttaagcttacattttattgtaataattgcagaagttacatctctaatttaactgtcag

upper sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 3
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagac--agaaacttc-gatattctataagtatatcggaattaaacttgtatac----tgacgctgtctgtcttgcctttttcag------------
||||||  || |||| ||  | | ||| |  || ||||| ||  |||| |||||||| ||||| || || || |||||||||||||| |||||||||||||| |||     | |||| | ||  || | |     | | |   | | | || | | |    | ||    | |||  |  || ||  |             
TCTACCAGTATCTGAGCTTCTGAGATTTGTTTTGTTTGCAAATTTGTCAATTGTTGGAATGAACGTGAGTTTAATGTGGAACTCTGTGGGATTCTATCAGgt-cagttttgggaactgctgactttttgttctccttttgctctcatattttttttcaaagttacaagttatgttctttctcttcaaactttgatgtcag

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|148969061|gb|EE019781.2|EE019781
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149088966|gb|EE178110.2|EE178110
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|50326262|gb|CO521388.1|CO521388
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|32919453|gb|CF024265.1|CF024265
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|37421524|gb|CF648462.1|CF648462
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|110223714|gb|EC905612.1|EC905612
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCCAGTCTTATGCATTCTGGAAATC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCC-AGTCTTATGCATTCTGGAAATC
EST: gi|71436369|gb|DR817419.1|DR817419
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
EST: gi|149090129|gb|EE179428.2|EE179428
EST:     TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC
genomic: TTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTC

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 2 RNA-Seq libraries.


Block sizes: 13 (upstream exon), 49 (downstream exon)
Score: 2

TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC


Block sizes: 16 (upstream exon), 49 (downstream exon)
Score: 5

TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacag ... cctttttcagATCGCAAAGCTGTGTATCATTCCAGTCTTATGCATTCTGGAAATCATGTTCGACAAAGTCCGTTACTCTAGAGATACAAAGCTCAGTATAGTGCTTGTCC




<