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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctccacgcactctgagttcaaacagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT

Basic information

species Zea mays
transcript GRMZM2G068392_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 5
gtaaatctccacgcactctgagttcaaacagtgttgt---cagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
|| || ||||||    ||| |||  |||||| ||| |   ||||  |||| |||||| |    |        || || ||||||||||| |||||||| ||||| | |||||||| ||||||||||| |||||| | ||||||||||||||||||||| |||||||||| ||||||||||| |
gtgaa-ctccacta--tctaagtctaaacagagttctgctcagaaacctgactgatcataggtc--------atccttaccagGAATCTCTGAAAAATATACTGATTATCTTTGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
-gtaaatctccacgcactctgagttc--aaacagtgttg--tcagatccctgtctgatc-ttttacctttttattattc-----tcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
  |    ||| |   | | | | ||   ||    ||     || |  |  | |||   | ||||  ||||  | | |||     |   |||||  |||| || |   || |  |  | ||||| ||| ||||  | || ||||||||| | ||||||||||||||||| ||||| || ||||||| ||| |
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
----------------gtaaatctccacgcactctgagttcaaa-cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                 ||| | |     ||   | |   |||  || |  | |    | ||  | ||| |||| | |||||    ||| |   |||||  |||| || |   || |  | || ||||| ||| ||||  | || ||||||||||| ||||||||||||||||| ||||| || ||||||| ||| |
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttga-ctttcaacttttccggattttt--cagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtaaatctccacgcactctgagt--tcaaa----cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                  || |  |  | ||  |  |  |  | |||    |||| |  | | |    |   ||   |||||    | | ||       | ||||  ||||||| ||  |  ||   || || || ||| ||||| |||| || |||||||||||||||||||||||  | ||||||||  | ||||   | |
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgt-ctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatctccacgcactctgagttcaaacagtgttgtcag-atc-cctgtctgatctt-ttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
    || |      |||    |    |    || |   |  ||| ||  | ||| |   |||  |   |  | |  |   |||||  ||||||  ||  || || |  | ||||| ||| ||||| | || ||||||||||| ||||||||||||||| ||||||| || || |||| |||||
--gtatgtgttgttacttgaggcatgagacttgatacaaacatcacccatttgaccaaattaaatggatcctgtattt--cagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT

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|44681890|gb|CK786938.1|CK786938
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTCGTTGCCAAGCTGAAATGCTGG
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTT--T-GCCAAGCTGAA-TGCTGG
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|113817914|gb|DW939072.1|DW939072
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGC
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGC
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                     gtctgat  putative branch site (score: 4)
                           tcttttacctttttat  CT-rich tract
                          atcttttaccttttta  TA-rich tract