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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_T02
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




















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: 40 (upstream exon), 46 (downstream exon)
Score: 140

GTATTGCCTATCGGGATCATCTGATTCAATGATAAGgtaaacacac ... tactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 145

GTATTGCCTATCGGGATCATCTGATTCAATGATAAGgtaaacacac ... tactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 173

GTATTGCCTATCGGGATCATCTGATTCAATGATAAGgtaaacacac ... tactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 151

GTATTGCCTATCGGGATCATCTGATTCAATGATAAGgtaaacacac ... tactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatgctgtggtaagtttgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC
                gtttgac  putative branch site (score: 151)
                                     tttttatttacttt  putative PPT
                       atcatagatacatatt  TA-rich tract