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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcctattctttactgagccccatacagaaaataacttctcttttatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT

Basic information

species Zea mays
transcript GRMZM2G114126_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 3
cttcctattctttactgagcc-ccatacagaaaataacttctcttttatctttcatgtgatgattca--tgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT
    ||||  |||    || |  | |   |   ||   | |||||     |    | | |  | ||   |||||||| | ||| |||    | |||||||||||||||||||||||||||  | |||||||||||||||||||| || || || |||||||||||||  ||||| |
---gctataatttggccagtcatccttttgtgcatccatactcttcctgttaaagtcttaatactcgattgctaatgatgttagctgcatgttctgaatgcagTTGATGGAATACTGTGAACTTTTAGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 3
--cttcctattctttactgagccccatacagaaaataacttctcttttatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT
  |  | || ||||   |  |||   |   ||  ||| |||    | ||   |  ||    ||||| |   | |   ||  |  || |     ||||   |||||||||| ||||   | ||||||||  ||||||||||||  |||||||||||||||||  | ||||||||  
gtcggcttactcttagttttgccat-tgttgatgataccttaatctgtagtgtcaat----tgattgaatttgaaaattgaaattgct-----tgaa-atagTTGATGGAGTACTCCTACTTGTTAGATCAAGCAGATGAATCAGAGGATCCATACATGCGGTTAGTTTATGCAA

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 3
----------cttcctattctttactgagccccatacagaaaataacttctcttttatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT
          ||   | || |||  || |     | |       || | |   ||||| | |  |||  ||   | || |   ||||| |  |||||   ||      |||||||||| ||||   |  |||||||  | ||||||||||||||||| |||||||||||  |||| ||||| |
gtttgcacagctctattttattttttgtgttttctgctttgttaaattgc---tttatttgtt-tgtattggcacttgattgagctttgaattgttcgaact------agTTGATGGAGTACTCCTACCTGTTAGATCAGGCAGATGAATGTGAGGACCCATACATGCGGCTGGTGTATGCAT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 3
cttcctattctttactgagccccatacagaaaataacttctcttttatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT
     |||     |   ||     || |      |  ||    ||  |   |  | |   |  |  | | |||| |   |  |||   ||||     ||||| ||||||||||   |  ||||||| |||||||||||||| |||||||| ||||||||  |||| |||||||
----gtatgtgccatctagttt-gtataagtttgatgtttatcttggtagattgtctctagcctgtttcaaatgttgcaaattgtgaatgcttgtgacagTTAATGGAATACTCCCACCTGTTAGATAAAGCAGATGAATGCGAGGATCCTTACATGCGATTGGTGTATGCTT

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|211354689|gb|FL118768.1|FL118768
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|211354687|gb|FL118766.1|FL118766
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAG
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAG
EST: gi|211354688|gb|FL118767.1|FL118767
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC-A
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|91055718|gb|EB166136.1|EB166136
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|67040089|gb|CO466344.1|CO466344
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|74236529|gb|DT644443.1|DT644443
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|26558339|gb|CA830574.1|CA830574
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|211354691|gb|FL118770.1|FL118770
EST:     TTCCAGTCATATTTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACCTGTGAGTTGTTAGAC
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATAC-TGTGAGTTGTTAGAC
EST: gi|211354686|gb|FL118765.1|FL118765
EST:     TTCCAGTCCTAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|149105113|gb|EE290596.2|EE290596
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|148961873|gb|EE012659.2|EE012659
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|78120437|gb|DV538821.1|DV538821
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|32801394|gb|CD953630.1|CD953630
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC
EST: gi|87155561|gb|DY400350.1|DY400350
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 105

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 215

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT
                     tgctaat  putative branch site (score: 92)
                                       ttcctgct  putative PPT
                              tttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcctattctttactgagccccatacagaaaataacttctcttttatctttcatgtgatgattcatgctaatgcttttacctgttcctgctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT