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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgcaaaacatctttggtgcacatatccctacagtttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC

Basic information

species Zea mays
transcript GRMZM2G063511_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 6
gtgagttgcaaaacatctttggtgcacatatccctacagt-ttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
|| ||  |  ||||| |||| |   || ||     ||  | ||  |||  | ||| | ||| | ||| |||  | |||||||||||||||| || || ||| ||||||| ||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||
gtaagcagtgaaacaactttcgaagacttactttgaccttgttttatctgattctgattttgcccttgtttcttatgcagTTTTTCATTGTATTATCGTGCTTGATATCTGTCTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACTTCTCCTGTCACTTACCAAGTCCTGGGCC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtgagt-tgcaaaacatctttggtgcacatatccctacagtttccatc--acactctaa-gttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
                  | || | | | |||| | ||   ||  | | |  || |  | || |||   ||   ||| |  | ||  | | |||  ||||||| ||||| ||  |||| ||||| ||||| ||||| || ||||||||||| |||||||| |||||||| || |||||||| || || || || || || |
gtgagactcaatttcccggggattctaccaaacttattaactgatcttcttgcttccatgtcgatcctgcatattaacgagtgcttctttgttgattgcagTTCTTCATCGTCCTGTCTTGCCTCATATCAGTCTCTGTAAACTTCAGCACATTTCTTGTCATTGGAAAAACATCTCCTGTCACATATCAGGTTCTAGGAC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 7
--gtgagttgcaaaacatctttggtgcacatatccctacagtttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
  | || |     || || | |||        ||  ||  | ||| | || | |   |       ||| ||| |  ||||||| ||||| || ||||| ||||| ||||| || ||||| ||||||||||| ||||| || ||||||||||| |||||||| ||||| || || || || |
gtgagaatgaagcaatatatgtggaatggtcttcattattgcttcta-catatttacaaacacaccttgttt-gaatgcagTTCTTCATCGTCTTGTCCTGCCTCATATCTGTTTCAGTAAACTTCAGCACGTTTCTCGTCATTGGAAAGACATCTCCTGTCACTTATCAGGTTCTAGGAC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------gtgagttgcaaaacatctttggtgcacatatccctacagtttcca--tcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
                                        |||       | |||  | |  | ||  ||  | ||   |  |||    |||| | |  ||  |  |  | ||||| | ||||||||  | || ||||||||||| || || || |||||||| || ||||| || ||||| ||||| |||||||| || ||||| |||||||| |
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatc--acctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S123_22V6.2 (Physcomitrella patens), 3'ss of exon 5
---------gtga-gttgcaaaacatctttggtgcacat---atccctac--agtttccatcacactctaagttttctct-tattttgtgtg-----cagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
         || | ||||   ||  || |  ||         |||  |    |  ||||||     | || ||  || |  |   ||||  |     ||||| ||| | ||| | ||||| |||||||| || ||||| ||||||||||| ||| | || ||||||||||| ||| | || ||||| ||||| || || |
atcatctgggtaatgttgactaatctcctatgtcagttcgggatcattgataaacttccatgcgcttttacgtgctcaccgtggcttgttgggatgccagTTCTTCGTCGTGCTTTCATGTCTGATATCTGTATCAGTCAACTTCAGCACGTTTTTAGTTATTGGAAAGACATCTGCGGTGACTTATCAAGTGCTTGGGC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ14247 (Selaginella moellendorffii), 3'ss of exon 5
gtgagttgcaaaacatctttggtgcacatatccctacagtttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
                     ||   || || | |    |   | |   |  |    |||| | |  ||   | ||||| | |||||  |  | || ||| |||| || || || |||||||||||||| || ||||| || || |||||||| || || |||||||||||| | ||||
---------------------gtaagcacatgctttttatccgcctatgaaacgcctttttttttctttgcctctgcagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

upper sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ20116 (Selaginella moellendorffii), 3'ss of exon 5
gtgagttgcaaaacatctttggtgcacatatccctacagtttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
                     ||   || || | |    |   | |   |  |    |||| | |  ||   | | ||| | |||||  |  | || ||| |||| || || || |||||||||||||| || ||||| || || |||||||| || || |||||||||||| | ||||
---------------------gtaagcacatgctttttatccgcctatgaaacgcctttttttttctttgcctttacagCTATTCATCATCCTTTCTTGCTTGATTTCCGTTTCTGTGAACTTCAGCACATTCCTTGTTATAGGGAAGACGTCGCCGGTGACTTACCAAGTCTTAGGCC

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|32931475|gb|CF036287.1|CF036287
EST:     TTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCTCAAGTTGTG                         TTTTTCATTGTGTTATCATGCCTGATATCGGTCTCAGTGAACTTCAGCACT
genomic: TTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACT
EST: gi|32932218|gb|CF037030.1|CF037030
EST:     TTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCTCAAGTTGTG                         TTTTTCATTGTGTTATCATGCCTGATATCGGTCTCAGTGAACTTCAGCACT
genomic: TTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACT

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: 49 (upstream exon), 49 (downstream exon)
Score: 88

CCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCTTCCTTGATGGCTTTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 75

CCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCTTCCTTGATGGCTTTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 100

CCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCTTCCTTGATGGCTTTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 127

CCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCTTCCTTGATGGCTTTTTGACTAACCAAAACGTCTTTGCTTTTAATTATACATCACAAGTTGTGgtgagttgca ... ttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatatccctacagtttccatcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC
                                 ttttctcttattttgt  CT-rich tract
                                 ttttctcttatttt  TA-rich tract