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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattacacaactctactcagtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT

Basic information

species Zea mays
transcript GRMZM2G162445_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 7
gtaaattacacaactctactcagtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
|||| |||   ||   |  |   | ||| |   || |      |||| | ||   |||| |        || || | ||| || |||||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| |||||||| |||||
gtaa-ttattgaaacttgtttcatacatatttgtttg------attcttatag--gtctgagcgatttcttgtggttagGTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAATGATCAGGACCGAGTGGCTAT

upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 7
gtaaattacacaactctactcagtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatt---------tctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
|||||| |  |  ||      | |  || |||||   | |  |||| |        ||| |  | |||||         |   |  ||| |||||||||||||||||||| || ||||||||||||||  | ||||| |||||||||||||| ||||| || |||||||||||||| || ||||||||
gtaaatcattcgtcttgggcta-tatatatgcataattctattattacatctgtcatctaagcaaaaattgtaatttctttcttctagGAGAAAGAAGGCTTGAAGCTGGGGCAATGGTTCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
--------------gtaaattacacaactctactca-gtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatt---------tctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
               |    || | |  | ||   |  |  || |||||   | |  |||| |        ||| | || |||||         |   |  |||||||||||||||||||||||| || ||||| ||||||||  | ||||| |||||||||||||| ||||| || |||||||||||||| || ||||||||
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------gtaaattacacaactcta--ctcagtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
                                    | || | |  || || |   |    | | |  ||   |||   | |||   | ||| ||  ||    | ||||   ||||||||| |||| || ||||||||||| ||||| || ||||||   ||| |||| |||||||| ||||||||||| ||||||||||| ||||||||||||||
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctat-ttctcattaaaatcaaattctcattttc--atcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT

upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 7
gtaaattacacaactctactcagtgcatgt--gcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgt--tcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
|||| |||    ||    | ||  ||||||  || ||  | | | | |    | | | |   ||      |   |||  ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| || || |||||||||||||| || |||||||||||||| || ||||||||
gtaatttatctcaccaggcccaa-gcatgttagcgttatt-tggcaattgcttcagactagtattctctttccttgtcatcagGAGAAAGAAGGCTAGAAGCTGGTGCCATGGTTCTTGCTGATCGAGGTGTTGTTTGTATTGATGAGTTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

upper sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------gtaaattacacaactctactcagtgcatgtgcattggtgtcgtat-tcctgtaaaagtctc--atgacaaatttctgtt--cagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
                                                                                                 ||  ||    |||  |     |  ||     ||||| | |||  ||   | |   |     |||    || |||     |||| || || ||||| || || || || |||||| | || || || ||  | || |||||||| |||||||||||||||| |||||  ||||||||| ||||
gtaagatatgtactccattctccttagttgtagccctaaggaagtgatttcatactgacgatacttggcggatgggagattatcgtaccattctcacaacctatcagacttcaaatt-tctatacaagttggtcttgtagatcacatgactattctgaatgtggtatctctacaaacagGAGAGAGGAGGCTAGAGGCAGGGGCGATGGTTTTAGCCGACCGCGGCATAGTGTGCATTGACGAGTTTGATAAAATGAGTGATCTTGACCGAGTTTCTAT

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|26457415|gb|CA828998.1|CA828998
EST:     TTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTG                         GGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCG
genomic: TTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTGgtaaattaca ... ttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCG




















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), 47 (downstream exon)
Score: 174

AGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGCAGAGGTTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTGgtaaattaca ... ttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 38

AGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGCAGAGGTTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTGgtaaattaca ... ttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

AGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGCAGAGGTTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTGgtaaattaca ... ttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 8

AGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGCAGAGGTTCATCTGGCGTTGGATTGACTGCTGCTGTGACTTCTGATCAAGAGACTGgtaaattaca ... ttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatttctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT
                                            tttctgttc  CT-rich tract
                                       acaaattt  TA-rich tract