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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 1
gtaagcacccca----ccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttcctttt-------tcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
|| ||    |||    | ||  |||||  ||| ||  |    || |   |    |   |  ||  ||   | |  | |  ||  |         |  | || |  |   | |    |||      ||     ||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||| |||||||||||||||
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagggaatgcagGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAACATCGAGTCG

upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
gtaagcacccca----ccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttccttt-------ttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
|| ||    |||    | ||  |||||  ||| ||  |    || |   |    |   |  ||  ||   | |  | |  ||  |         |  | || |  |   | |    |||      ||     ||||||||||||||||||||||||| || ||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||| ||||||         
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------

upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcggg--atttctccgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
             |  | |  ||   || | |   |||| |  || | ||    ||| |  |   |  | |  || |||||  ||  ||   || ||   | || |         || |    |||||||||| ||||| ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || || |||||||| |||||||| |||||||||||||||
------------gcacgtcttcct--attctgttccctt-tcactcagtcctctgcgtccggttagttactgttctgttccgattcgtta--ctaat--tgatgattactaccattgac----aatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG

upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggc---gcgcgggatttctccgttcctttttcttcttctgatgac-gctgctcgg-gttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
                             || ||||||  || | |   || || |  |   |||   ||||  |   |    | |||| || |   | |   ||  | |  | || ||   | ||| |||||||| || || ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || || |||||||| |||||||| ||||||||||| || 
--------------------------gcacgtcctcct-attcccttccctttcactcctctgcgtccgattagttactgttctattctgctccgattcattactaattgatgattactattgacaa-tgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC

upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S162_10V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctct-cgcggcgcgcgggatttctccgttcctttttcttcttctgatgacgc-tgctc--gggttttctggcgtcaaatgca---gGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
                                      ||   |  || | |  | |     ||||| ||| |  | | |||  |||| ||  |  ||  | | |||   | || ||     |    ||||   |||| ||  |  |||| || || ||||||||||||||||||||||| ||||||||| | || || || ||  | ||  |  | || |||||||| || || 
-----------------------------------ttgtgcaacggaaccacggctcacaatgcggggtttgtgggatgcttaatcttttttaggcgagacatcctccaagattctcatagttttgctgcaacagGGTACGCAGATACACTATATCCGTGTTCGTCGGGGACGAGAGCGGAATGATCAACAGAATTGCTGGAGTTATTGCACGACGTGGTTACAACATTGAATCT

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|211258838|gb|FL034314.1|FL034314
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211261271|gb|FL034325.1|FL034325
EST:     CCCCCGTGGCTGTGGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: CCCCCGTGGCTGTG-TCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|148959834|gb|EE153063.2|EE153063
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258845|gb|FL034321.1|FL034321
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258848|gb|FL034324.1|FL034324
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|76285096|gb|DV024664.1|DV024664
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|149075260|gb|EE163764.2|EE163764
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258839|gb|FL034315.1|FL034315
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211261273|gb|FL034327.1|FL034327
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258836|gb|FL034312.1|FL034312
EST:     CCCCCGTGGCTGTGTCGGCTGTCGCNNCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: CCCCCGTGGCTGTGTCGGCTGTCGCC-CCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258843|gb|FL034319.1|FL034319
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|148949305|gb|EC894756.2|EC894756
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|149087824|gb|EE177122.2|EE177122
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT

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

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 56

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 21

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
               ttctgat  putative branch site (score: 76)
      tttttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG