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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG

Basic information

species Zea mays
transcript GRMZM2G112672_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 1
gtacgtccaagc-cgcttccccgtttcc----gttgtctccttcaattc----ttcgtccgtagtaccgtgatcgattgtcttccgtt--tgtcttactgcctcgtctgcgtctaaaac---------------tttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
||||||||   | | ||  | || || |    |  || | ||| | |      |   ||  | | || |  ||  ||||| |||| ||  ||| |  | ||       || |                      | | | ||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||||
gtacgtcctctctctctctctcgcttgctcgtgcagtgtacttgagtgtcgattgtttcacttgaactgaaattaattgtgttccctttttgtttcgcggcgcatgtggcattgggggtggtggtctgctcgtttgtgcgtgcagTTAGTGTGAGCGAGGTTGAGGCGTTGTATGAGCTGTTCAAGAAGATCAGCAGCGCGGTGATCGATGACGGACTGATCAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                   | ||||    | ||   ||    |  |  |    |  | | | |   || |        ||  |  | |      | |  || |   | | |     ||||||| || || ||| | || ||| |||||||| |||||||||||||||||||||| ||||||||||| || || || || |||
-----------------atctgtttttactctcaatttt--cttctttttatcaaaatcataaaaaataggaaagaaattaacaaaataagatatttatgtgttttattgttgacacagTTAGTGTAAGTGAGATTGAAGCACTGTATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaatt--cttcgtccgt-agtaccgtgatcgattgtcttccgtt--tgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                        || ||| | ||  ||||||  |||| |  || |  | | | |   ||||        |  |  |  | |      | |  || |   | | |   ||||||||| || || ||| | || ||  | |||||| |||||||||||||||||||||| ||||||||||| || || || || |||
------------------------tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
        || | | |     ||     |        | | || | |   | |  | | || | | |   ||||   |  | |||    | |    ||  |     | |||  |||||||||| || || ||| | || ||| |||||||||| |||||||||||||||||||  || || ||  | ||  | || |  |||
--------aaactgttat---gtaggaatgaatctgcttagttttac---catttttcagttaccaaggctcttat-taagacttggaacataacttgtttt----attttcactgcagTTAGTGTAAGTGAGATTGAAGCACTGTATGAACTATTCAAGAAGATCAGCAGTGGAGTAATGGACAAAGGATTAATTACTAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccg-tgatcgattgtcttccgtttgtcttactgcctcgtctgc-gtcta---------aaactttacct------gcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
||| | || | |  |||| |   |    || | |  ||   ||    ||    ||   || ||    |   | |   |  ||    | |   || ||||  | |||          || ||    |      |||||||| ||||| ||  | || ||  | ||||| || || ||||| ||||||||||| ||||||||||||||||| || ||||||
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgt-agtaccgtgatcgattgtcttcc---------------gtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                               ||  | | |  | |||     || | ||| | |   | | |     |   |  | |||  |  | |||  |||                   | | |||| |||  |  |   | |  |    |||   ||||||||||||||| ||  | |||||  | ||||| ||||| ||||| ||||||||||||||||||||||||||||| || ||||||
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                                                                                                                       |||| || || ||  | || ||| | ||||||||||| |||||||||||||||||||| ||||||||||| || |||||||||
-----------------------------------------------------------------------------------------------------------------------ttAGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                    | || |       | ||   | | | | | |     ||  |  |       | |       |  |||||     | |   | |     ||    | ||||||| || || ||  |||||||| | || || ||||| |||||||||||||| |||||||||||||| || ||||||||||||
-------------------tcattcctacctaatgctaatagtttgctttctgccaactcttttaatgaaccattaaagcattgtactgaagattgtaatttttttctttccaatacagTTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAG

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|5846848|gb|AI999931.1|AI999931
EST:     GCTAGGGAGACCGNGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA
EST: gi|6194508|gb|AW146612.1|AW146612
EST:     GCTCGCTAGGGAGACCGNGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA
EST: gi|211071789|gb|FK958795.1|FK958795
EST:     TGCTCGCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: TGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA
EST: gi|211071790|gb|FK958796.1|FK958796
EST:     TGCTCGCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: TGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA
EST: gi|5325037|gb|AI783228.1|AI783228
EST:     GCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 134

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

GTGAAGCAGCTCCTTGCCGTGCTCCTCAAGTGCTGCCACATCGACCTCAAGCAGCCCAACGGCCTAGATGATCCGGAGGTGCTCGCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                                   gtctaaa  putative branch site (score: 146)
                                           ctttacct  CT-rich tract
                                      taaaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT