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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggctaagaacatgtctatcgatgacgcatgaatcggacgttttctgttttacagcgtggtagtggtgctaaattcctgccatgcgggttcatgtgtgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT

Basic information

species Zea mays
transcript GRMZM2G128971_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128971_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 4
gtgaggctaagaacatgtcta---tcgatgacgcatgaatcggacgttttctgttttacagcgtggtagtggtgctaaattcctgccatgcgggttcatgtgtgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT
|| |||| |||| | | |  |   ||  |  |   || ||  || ||| | | ||||  |   |  ||      |||||||||||   || ||||||||||    |||| ||||||| ||||||||||||||   ||| ||||||||||||||| ||||||||||||||||||| | ||| ||||| ||  | |||||||| || || ||||
gttaggccaagagcttcttgacattcattatcaactgtattagaggttct-tattttgtaatatcata------ctaaattcctggtttg-gggttcatgt---ctatgcagTTTGCAAGGAGTCCAGGGAAAAAAGGTTCACACTTCAACCCAAGCAGTGATCTGTTCCAACCAAATGAGAAGAAGGATGTGATAACATCAACTGCATCCT
















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|94473265|gb|EB702223.1|EB702223
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|94473191|gb|EB702149.1|EB702149
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|33099402|gb|CF059362.1|CF059362
EST:     GCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: GCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|32924103|gb|CF028915.1|CF028915
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCACGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|71449312|gb|DR830362.1|DR830362
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|149098532|gb|EE184518.2|EE184518
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|211331124|gb|FL341574.1|FL341574
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|149067507|gb|EE157713.2|EE157713
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|78088570|gb|DV516963.1|DV516963
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
EST: gi|94473190|gb|EB702148.1|EB702148
EST:     AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTG                         TTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT
genomic: AACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGAT

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), 44 (downstream exon)
Score: 43

CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

CTACCAGAGAGGCTGTACAAAAGCCTGGACTTTATGACTAGGAAACTGCGGTTCACCATGCCGTTCCCCTTGCTCGCGTTCCCGTTATACTTGgtgaggctaa ... tgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagcgtggtagtggtgctaaattcctgccatgcgggttcatgtgtgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT
               tgctaaa  putative branch site (score: 125)
                  taaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggctaagaacatgtctatcgatgacgcatgaatcggacgttttctgttttacagcgtggtagtggtgctaaattcctgccatgcgggttcatgtgtgttatgtagTTTGCGAGGAGTCCAGGGAAGTCAGGATCACACTTCAACCCAGGCAGTGATCTGTTCCAACCTACTGAAAAGAATGACATCATAACATCGACGGCGTCCT

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