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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagtatatgttactgcagttagttggtgcaatttttttcttgtgccttcaatttgattgccttgtatccatgtacttacggatcccttctctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT

Basic information

species Zea mays
transcript GRMZM2G022019_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022019_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 1
-----tcagtatatgttactgcagttagttggtgcaatttttttcttgtgccttcaatttgattgccttgtatccatgtacttacggatcccttctctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT
       | |||  | ||||   |  | ||| |     |||| || | |   | ||     ||   |||   | ||| ||  | |       ||   || || ||| |||||||||||||||| |||||||||||| || | |  ||||||||||||||| ||||||||||||| ||||| ||||| ||||||||||||||||||
cctgcctattatcggatacttttga-atttgattgtccttttatcctatatgtgcaggc--atgatcttcctttcatttaaatccc--cttatttcttgctgcagCTTGTATGATCAGATTTTCCGTCCAAGCAAGGTGACAGTAAATGCTGATTTTCATTTATTCAAGGCTGGTGTAGAACCAAAGTGGGAAGACCCAGAGTGT
















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|211334027|gb|FL370162.1|FL370162
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211323606|gb|FL396586.1|FL396586
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211254448|gb|FL405697.1|FL405697
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|26558254|gb|CA830489.1|CA830489
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211536036|gb|FL385929.1|FL385929
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211533212|gb|FL395811.1|FL395811
EST:     A-CTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|50336177|gb|CO531303.1|CO531303
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|21987193|gb|BQ778721.1|BQ778721
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211515995|gb|FL388516.1|FL388516
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211311470|gb|FL411468.1|FL411468
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211077767|gb|FL430526.1|FL430526
EST:     AC-TCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211368575|gb|FL387082.1|FL387082
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCCTGATT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGC-TGATT
EST: gi|211151625|gb|FL390476.1|FL390476
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211027895|gb|FL424771.1|FL424771
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|78026174|gb|DV494561.1|DV494561
EST:     CCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: CCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211115395|gb|FL414256.1|FL414256
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|71437159|gb|DR818209.1|DR818209
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211413496|gb|FL407162.1|FL407162
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211254363|gb|FL402651.1|FL402651
EST:     ACCTSCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGT
EST: gi|50322672|gb|CO517798.1|CO517798
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|32164823|gb|CD670141.1|CD670141
EST:     GAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: GAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|71758459|gb|DR956396.1|DR956396
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|31558353|gb|CD527565.1|CD527565
EST:     CGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: CGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211406227|gb|FL424174.1|FL424174
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|32933632|gb|CF038444.1|CF038444
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211478942|gb|FL383623.1|FL383623
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|16925812|gb|BM078880.1|BM078880
EST:     ACATCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|22935572|gb|BU571847.1|BU571847
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|91049925|gb|EB160343.1|EB160343
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT
EST: gi|211020161|gb|FL408602.1|FL408602
EST:     ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAG                         CATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAGTGCTGATTT
genomic: ACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTT

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: 201

CCTTCTGGTACGACATCCAGACGAAGACCAAGTCCGGGGCTGCGTGGGGCACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 244

CCTTCTGGTACGACATCCAGACGAAGACCAAGTCCGGGGCTGCGTGGGGCACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

CCTTCTGGTACGACATCCAGACGAAGACCAAGTCCGGGGCTGCGTGGGGCACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 145

CCTTCTGGTACGACATCCAGACGAAGACCAAGTCCGGGGCTGCGTGGGGCACCTCCCTCAAAAAGGCCTACACCTTCGACACCGTTGAGGAGTTCTGGAGgtacgttggc ... tctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcaatttgattgccttgtatccatgtacttacggatcccttctctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT
                            tacttac  putative branch site (score: 145)
                                      tcccttctctgttgt  putative PPT
     aatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagtatatgttactgcagttagttggtgcaatttttttcttgtgccttcaatttgattgccttgtatccatgtacttacggatcccttctctgttgtagCATGTATGATCAGATTTTTCGTCCAAGCAAGTTGTCTGGGAATGCTGATTTTCATCTATTCAAGGCTGGAGTAGAGCCAAAATGGGAAGACCCAGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - actgcag
- - - - - - - - - - - - tggtgca
- - - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - gccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccatg