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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaacttctagtgttacttctgttcacacacatttattgcttgacttcgtaactttaacttcgatgaacaaaatgtggaaccatttctggacct...

Basic information

species Zea mays
transcript GRMZM2G565140_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G565140_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 5'ss of exon 3
GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaacttctagtg-------ttacttctg--ttcacacaca-tttattgc-ttgacttcgtaactttaact-tcgatgaacaaaatgtggaaccatttctggacct
 || ||  ||| |||||| ||||||||||||||||| |||||||| ||||| | ||  ||||| ||||| | ||| || | |||||||||| | ||||||||||||   |    |  |        || ||  ||  || ||||| | |  ||||| | || |  | |||| || || |   |    ||||||      |            
ACCTCCAAAACGTCAAACCTTGATGTTCTCTGCGACTATGCCAACTTGGATTCAGAGACTCACCCAGAAATACCTTAAGAATCCTGTTACAATTGACCTTgtgagttttatacttgctaaactcctttgctcttggttttacacataatccattgcatagattgtggaactatatctgtttttatttaaaatgcactctc------------
















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|32842833|gb|CD982514.1|CD982514
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842842|gb|CD982523.1|CD982523
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842824|gb|CD982505.1|CD982505
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842589|gb|CD982270.1|CD982270
EST:     AAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: AAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842460|gb|CD982141.1|CD982141
EST:     TACGGAAGCTCACCCAGAAGTACCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842456|gb|CD982137.1|CD982137
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842583|gb|CD982264.1|CD982264
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842809|gb|CD982490.1|CD982490
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842391|gb|CD982072.1|CD982072
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842737|gb|CD982418.1|CD982418
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842485|gb|CD982166.1|CD982166
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCCCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842566|gb|CD982247.1|CD982247
EST:     GTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: GTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842765|gb|CD982446.1|CD982446
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842619|gb|CD982300.1|CD982300
EST:     TTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842750|gb|CD982431.1|CD982431
EST:     TACGGAAGCTCACACAGAAGTTCCTCACCAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32842646|gb|CD982327.1|CD982327
EST:     TACGAAAGCTCACCCAGAAGTTCCTCAACAGTCCTGTTCCAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
EST: gi|32841848|gb|CD981529.1|CD981529
EST:     TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTT                         GTTGGTGAGGATGACCAGAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC
genomic: TACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTC

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: 176

GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG


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

GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCCCGCAACATCAAACATTGATGTTCTCTGCGACAATGCCAACATGGATACGGAAGCTCACACAGAAGTTCCTCAACAGTCCTGTTACAGTGGACCTTgtgagtgcaacttctagtgttacttctgttcacacacatttattgcttgacttcgtaactttaacttcgatgaacaaaatgtggaaccatttctggacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaaa