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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtcgccccagcgctagctagattcagcattgagctcacctgttgtgtttgtggttactgactgttgcttctttgcacctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT

Basic information

species Zea mays
transcript GRMZM2G375002_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 6
---gtactgtcgccccagc--gctagctagattca--gcattgagctcacctgttgtgtttgtggttactgactgttgcttctttgcacctcca--tccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT
   ||  | | |    ||   |  |  | || |    || ||||||||   ||  |||    |||||||||| || |||| ||||||   | ||  | |||||||| || ||||| || || || || |||||||||||||||||||| |||||||||||||||| |||||| |||| |||||| |||||  |||| ||||
ccggtgatatagttgaagggagtaaaatggacttgttgcgttgagctccattgcggtggc-atggttactgattgctgctgctttgcctttgcaactgcagAACATCAAGGCAGTTTTCGATGCTGCGATTAAGGTGGTTCTCCAGCCTCCAAAGCAAAAGAAGAAGAAGAAAAAGGCGCAGAAAGGATGTGCCATCTTGT

upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 8
gtactgtcgccccag-cgctagctagattcagcattgagctcacctgttgtgt---ttgtggttactgactgttgcttctttgcacctccatcca---gAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTG---CAGAAGGGATGCACCATTTTGT
||| |  |     || |  || ||  ||  |   || | ||  |       |    |||    | ||||   || ||   |      ||  | ||   |||  | |||||||||||||| || || || ||||| |||||||||||||||||  | ||||||| ||||||||        ||||| || ||  | ||     
gtattaacctgagagtcaatatctttatctaatctttacctgtctaaaaccgccaattgaatctgctgatgattcctatatctgttatctgttcaacagAATGTGAAAGCAGTGTTTGATGCGGCTATCAAGGTCGTTCTCCAGCCACCAAAAAACAAGAAGAAGAAGAAGAGAAAATCTCAGAAAGGTTGTTCTATAC---

upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 6
gtactgtcgccccagcgctagcta--gattcagcattgagctcacctgttgtgtttgtggttactgac----tgttgcttctttgcacctcca--tccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT--
|||      |   |  | |   ||   ||  | |    |       | | ||||| ||||  |||| |    | ||  |  ||   | |||    | |||||  |||||||||| |||||||||||||| |||||||||||||| ||||||||||| ||||||| |||||| ||    || |||   |||  |||| |||  
gtatgacatcgatattggtgtttatcaatcaaactggaaataagggtttcgtgttagtggagactgtcatcttattattgtttgctatctcttattgcagAATGTAAAAGCAGTTTTTGACGCAGCAATCAAGGTGGTTCTCCAACCACCAAAGCAGAAGAAGAAGAAGAAAAAA---CAAAAGAATTGCGTCATTCTGTGA

upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
---------gtactgtcgccccagcgctagctagattcagcattgagctcacctgttgtgtttgtggttactgactgttgcttctttgcacctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT--
         ||    | || | |||  | | |||||    |    |  |  | | |          |  |    ||| ||| |   ||    ||  | |||||  | |||||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||| ||| || ||    || |||   ||   |||  | |  
ggtcacaacgtgtcatagctctagcaattg-tagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAAAAA---CAAAAGAACTGTGTCATACTCTGA

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|211386802|gb|FL474297.1|FL474297
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|32935747|gb|CF040559.1|CF040559
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCCCCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|5055407|gb|AI734294.1|AI734294
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|6973662|gb|AW438236.1|AW438236
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|37374347|gb|CF623524.1|CF623524
EST:     AGCTAATTGGTGCTGCCGCGTACATCGAATGCAGTTCAAAAATCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|71302719|gb|DR787472.1|DR787472
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCCCCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|16926993|gb|BM080061.1|BM080061
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|8383272|gb|BE056215.1|BE056215
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|67018898|gb|CO447647.1|CO447647
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|16925708|gb|BM078776.1|BM078776
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|5510771|gb|AI857155.1|AI857155
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|78107806|gb|DV526224.1|DV526224
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCCACC
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCC-ACC
EST: gi|37391181|gb|CF632832.1|CF632832
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAATCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|16918068|gb|BM073562.1|BM073562
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTT-ACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|16925543|gb|BM078611.1|BM078611
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|58029957|gb|CX725384.1|CX725384
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|4646692|gb|AI491552.2|AI491552
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCNCCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|28930831|gb|CB334192.1|CB334192
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|10697643|gb|BE997367.1|BE997367
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|28986594|gb|CB351213.1|CB351213
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|101401925|gb|EB822590.1|EB822590
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTTTCCAGCCCCCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|18174791|gb|BM350179.1|BM350179
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCA
EST: gi|32828059|gb|CD967737.1|CD967737
EST:     AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG                         AACATAAAAGCAGTGTTTGACGCAGCAATTA
genomic: AGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTA

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: 189

GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 349

GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

GGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAGgtactgtcgc ... ctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcacctgttgtgtttgtggttactgactgttgcttctttgcacctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT
                      tactgac  putative branch site (score: 213)
                                  cttctttgcacctcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtcgccccagcgctagctagattcagcattgagctcacctgttgtgtttgtggttactgactgttgcttctttgcacctccatccagAACATAAAAGCAGTGTTTGACGCAGCAATTAAGGTGGTTCTCCAGCCACCAAAGCAAAAGAAGAGGAAGAAGAAGGTGCAGAAGGGATGCACCATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG