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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC

Basic information

species Zea mays
transcript GRMZM2G167999_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
-------------------gtaaacacac-agctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggt----aagtt---tgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                    |   ||| | || |||    | |         | | ||   || |  | |      |  || |    ||||    | ||||| |   | || || ||| |  | |||||||| |||||||||| ||||||||||| ||| |||||||||||||||||||||||||||| || ||||| ||||||||||||||| | ||| ||||||| || 
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
||||   ||||  | |    |   || ||| ||  | | |  ||||           ||||||     ||||    ||   |  | |   | ||| || |  || || |||||| |||| |||||| | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || 
gtaa-tgcacacatatggagttataagcatttctatttgttttgttt---------ttgtggt-----tgac----taataatctgtcggtgtttcctct--agGCTTTGGGATATAGGTCAGCAGAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 7
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                            ||     | | |  | |||  |||| | || |     |||| |     ||   |  |     | ||| | |   || || |||||||| || ||||| || ||||| ||||||||||| || ||||| |||||| ||||||| |||||||||||| |  ||||| ||||||| || 
-------------------------gtaatgcgtgtatatggttttataataatttcttt---ttgttttatggtttactaatctcaccatcttt-catcatagGCTTTGGGATCTTGGTCAGCAACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
||||   ||||  | |    |    ||||| ||  | | |  ||||           |||  |  |||||||       |||     |   | || | |   || || |||||| |||| |||||  | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || 
gtaa-tgcacacatatggagttattaccatttctgtttgttttgtt----------ttgttttgtgtttgac-----taataatctgtccaactttcctcatagGCTTTGGGATATAGGTCAGCAAAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G40440.3 (Glycine max), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
||||   ||||  | |    |   || ||| ||  | | |  ||||    |   |  ||||||    |    || ||   ||||| |||    ||       || || |||||| |||| |||||| | ||||| ||||||||||| || ||||| ||||||||||||||||| || ||||| || |||||| ||||||| || 
gtaa-tgcacacgtatggagttataagcatttctatttgttttgtt----ttgtttttgtggttgacta---attatctgtacatctttacgctt-------agGCTTTGGGATATAGGTCAGCAGAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTCGCCAGCACCCCAGCATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G40360.1 (Glycine max), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
||||   ||||  | |    |    ||||| ||  | | |  ||||           ||||     ||||||    ||   |  | |   | ||| | |   || || |||||| |||| |||||| | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || 
gtaa-tgcacacatatggagttattaccatttctgtttgttttgtt----------ttgtg-----tttgac----taataatctgtccatcttt-cctcatagGCTTTGGGATATAGGTCAGCAGAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatg-ttagcataaatgctgtggtaagtttgacatcatagat---acatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                             |||   | | || |   ||| | | |  || || ||  |    |||   || |   ||   || | | ||  | |  ||||||||||||||||| |||||||| ||| ||||| | ||||| |||||||| |||||||||||||| |||||| |||  ||  ||||| ||||||| || 
----------------------------gtctgtatttttcttaactagtacata-actatgatagctgaatcatttcagttctaactggttctaaattcatgtttagACTATGGGATCTAGGTCAGCAGCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagca---taaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
   | ||| ||  |  || || |    | | |   ||  |    |||      | | ||||       |||   || | |   ||||| | | |    | ||  ||| ||||||||||| || |||||| | || || ||||| ||||| |||||||| |||||||| ||||||||||||||||| ||  ||||| | ||||| || 
---atcacgca--ttcaatatatgtttcgtttatttccttataattaatccttttagtgcttcatgtggttgatcaacct--gtacatctctcttcacatttcacagGCTATGGGATCTTGGTCAGCAGAGATGCGTGCATTCCTATGCCGTGCATACAGATTCTGTCTGGGCACTTGCAAGCACCCCAACATTTAGCCATGTTTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S28_153V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtaaacacacagctctaacatc-tcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
   | | |     ||      ||  |     ||||   ||   ||   ||| |  | | || |  ||  | |||      | ||   |  |||| |  || |  ||| || |||||  | || || || |||||  ||||||||||||| || || | ||||||||||||||| ||||||||||| ||  ||||  ||||||| || 
gtatgagctagttgccggtttataattgcttatctgattcgaccac-ctagtaagagttcttttctacttatga-----gaaatctctcattttctgcacat-acagGCTCTGGGACTTGGGGCAACAACGTTGCATTCATTCTTATGCGGTTCACATTGATTCTGTTTGGGCCCTTGCAAGCACGCCATCATTCAGTCATGTGTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S84_75V6.1 (Physcomitrella patens), 3'ss of exon 1
---gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
   || ||   |     ||  | |  | |   |   | | |    || ||   |   | | ||  |||   || | |  | ||   |       | | || || ||| || |||||||||||||| || |||||  ||||||| || || || || || ||||||||||||||  |||||||||| ||  ||||  ||||||| || 
gaagttaatgtattaacctgccgttgccaaatttgactttttatctgataattttg-tacggtattaa---tggctt--ttgactaacgaggaaactcacgtt-cagGCTCTGGGATCTAGGACAACAACGTTGCATTCATTCCTACGCGGTTCACACGGATTCTGTTTGGGCTTTTGCAAGCACGCCATCATTCAGTCATGTGTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S69_10V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
   |      |    ||| ||  ||        | |   || |  |||      |  | |       |   ||| | |  | | | | |||   || | ||||| || |||||| ||||||| || || ||  ||||||||||||| || ||||| |||||||| ||||| ||||||||||| ||| | ||  |||| || || 
---atttggtaaggttaatattccacgttgaaacattcttcctcgtagtggttgtaatttttcttcctactcattagaagtccct-tattttcataatatgcagGCTTTGGGATTTAGGACAACAACGCTGCATTCATTCTTATGCAGTTCATACAGATTCTGTCTGGGCTCTTGCAAGCACGCCTTCCTTCAGTCACGTGTAT

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ37688 (Selaginella moellendorffii), 3'ss of exon 7
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                                             |||| || |     |   | ||||   ||    ||   |||  |    | | |   ||| || |||||||| || ||||| |||||||||||||| ||||||||||| ||||| || || ||| || | || |||||  |  | ||| |||| || |||
--------------------------------------------gtagc-tatacatcata-catgttt---atttccgactgataactagcgtcaatgc-cagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCATATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC

upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ15001 (Selaginella moellendorffii), 3'ss of exon 7
gtaaacacacagctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                                             |||| || |     |   | ||||   ||    ||   |||  |    | | |   ||| || |||||||| || ||||| |||||||||||||| ||||||||||| ||||| || || ||| || | || |||||  |  | ||| |||| || |||
--------------------------------------------gtagc-tatacatcata-catgttt---atttccgactgataactagcgtcaatgc-cagGCTTTGGGATCTTGGGCAGCAACGTTGTGTTCATTCGTATGCTGTGCACACTGACTCAGTGTGGACAATGGCGAGCACATCCTCTTTTAGTCACGTTTAC

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|71433407|gb|DR814457.1|DR814457
EST:     GTATTGCCTATCGGGATCATCTGATTCAATGATAAG                         ACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATAC
genomic: GTATTGCCTATCGGGATCATCTGATTCAATGATAAGgtaaacacac ... tactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                gtttgac  putative branch site (score: 4)
                                     tttttatttacttt  putative PPT
                       atcatagatacatatt  TA-rich tract