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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctaacctaatgcgttgttcatgaggctactctgctgctcttatttgtctaattcaactccatatgccctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG

Basic information

species Zea mays
transcript GRMZM2G144254_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
---------------gtatg-gctaacctaatgcgttgttcatgaggctact-------ctgctgctcttatt-tgtctaattcaactccatatgccctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
               | | |  ||||||||| ||||||||| |  | || ||       |   |||  | ||  | | |  |  || |  |  | | || ||| ||||||||  ||||||||||||||  ||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || ||||| || ||||||||||
gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG

upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 10
----------------------------------------gtatggctaacctaatgcgttgttcatgaggctactctgctgctcttatttgtctaattcaactccatatg--------ccctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
                                         |     |   ||||||  ||| | | |   ||  | ||  | |  | |||| | |||   | | |  | |         || ||    ||||||   || |||||||||||  ||||||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| || |||||||||||| 
gtaaggctttttcttgggtaaagattctttgttgggctttatcaatttgtgctaatgttttgatgaggtaact-ttttgaagttaatttttgacaaatgtgaatgctaacgaagccttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTA

upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 10
-----------------------------------gtatggctaacctaatgcgttgttc--atgaggctactctgctgctcttatttgt--ctaat-------tcaactccatatgccctatgtg-acagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
                                   |  |    ||  |     | ||||   ||| ||  ||| |       | |||| |  | |||         ||| |  | |   | |  ||  ||||||   || |||||||||||  ||||||| ||||||||||| || |||||||| |||||||| ||  | ||||| |||||||| ||||||||||||||| 
gtaaggctttttctttggtaaagattctttgttgggctttatcaatttgtgctgatgttttgatggggtaactttttgaagttaatttatgacaaatgtgaatgctaacccggtcttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTA

upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------gtatggctaacctaatgcgttgttcatgaggctactctgctgctcttatttgtctaattcaactccatatgc-cctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
                           ||   |  ||| |||||  ||  | |       |    ||| |    |||           |||  | | |||  ||||||  ||||||||||||||| |||||  ||| ||||||||| || || |||||||||||||| ||||||||||| |||||||| |||||||||||||   
gtaaaaaaaaacctcaagctactgaaatattttggtgctttgtt-gtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA

upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 9
-------------gtatggctaacctaatgcgttgttcatgaggctactctgctgctcttatttgtctaattcaactccatatgc---cctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
               |  |  |    ||    |   |  ||    |  |  |      | | || |  ||   |     ||||     |   |    ||||||| ||| ||||| |||||||||||||| ||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| |||||||||||||
agagagaaaaagaaaaaagaaacaaaaaaaaatcaatgctgcaattggttggacatgttaaattttgcaaacaactgatatatattatctccttctgcagATGGCAAGGTTGAACGAAGGGTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTG

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|5296213|gb|AI782893.1|AI782893
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|6227147|gb|AW155676.1|AW155676
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|113701592|gb|EE679096.1|EE679096
EST:     TGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: TGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|211277446|gb|FL309933.1|FL309933
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|19822362|gb|BQ048386.1|BQ048386
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|19822356|gb|BQ048380.1|BQ048380
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
EST: gi|78022546|gb|DV490933.1|DV490933
EST:     GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGG                         ATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATTGTTCTTCTGTTTCTGTGTACCGCTGGATTTTGGgtatggctaa ... tatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctactctgctgctcttatttgtctaattcaactccatatgccctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
                      gtctaat  putative branch site (score: 3)
                ttatttgtctaatt  TA-rich tract