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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcaccagtctatgttcttgttcttttttttcatcaacatcgcgtttcctgaattttcttatatcaggtagggtaacataccttgtctcttttattatattcaatcag

Basic information

species Zea mays
transcript GRMZM2G435373_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 4
GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcaccagtctatgttcttgttcttttttttcatcaacatcgcgtttcct---gaatttt---cttatatcaggtagggtaacataccttgtctcttttattatattca-atcag---------------------------------------
||||||||||||| ||||| | |||||||| |||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||||||||||     ||   |  | || | | || | ||||||| | |||| | ||||||   |  ||||   ||| ||||     || |     | ||    |||  | ||||    |    ||                                       
GGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTGACAAAGTATTTGTCATTCAAAGCTGTCGATGGAAGCTATGTCTTCAGCAAAGGGAAGgtaa----catcttcagctcatttcctctgttttcattagcatcacatttcctctagtgttttatacttttatctaagtggttgttggatctatattctgatcttattcctatgctagcagtgtaacatgcacttttctatttttgctgtcaaccag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 4
GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgta--gtcaccagtctatgttcttgttct------tttttttcatcaacatcgcgtttcctgaatt-ttcttatatcagg--tagggtaacatac-cttgtctcttttattatattcaatcag------------------
||||||||| ||||||||  | ||||| || |||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||||||||||   ||  |||  ||||||  | || |       |  | |   | | |  |  ||  || | |  || ||| |||     |  ||| |  |   ||| |  || |||  |||  |  |                     
GGCAAATGGCACATTGGTAAGGACCCTGATTCACACTGATGTGACAAAGTATTTGTCATTCAAAGCTGTTGATGGGAGCTACGTCTTCAGCAAAGGGAAGgtaacatcttcagcttatgttagtcttttaatagcatcatatttccgatagtgttttctctaagtggttgttagatctatattctggtgatctgttcttattcctattaacatacccttttctattttcattgtcaatcag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 4
GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcaccagtctatgttcttgttcttttttttcatcaacatcgcgtttcctgaattttcttatatcaggtagggtaacataccttgtctcttttattatattcaatcag
||| || |||    | || |||   ||||| ||||| |||||||| ||||||||| | |||||||| || ||||| |||| ||| |  | ||||||||||||| ||   |    |  |      | |   ||   | |       | ||| ||   ||||   |                                               
GGCTAACGGGCAGCTCGTCCGAGTTCTCATTCACACCGATGTGACCAAGTACTTGGCTTTCAAAGCCGTAGATGGAAGCTTTGTGTATACCAAAGGGAAGgtaatcgaaaacaaaaatgtcgagtttcaattcaaacctttgggccattttct---tttttccag----------------------------------------------

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|149050331|gb|EE048608.2|EE048608
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|32846965|gb|CD986646.1|CD986646
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064222|gb|FL094759.1|FL094759
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|31612099|gb|CD568721.1|CD568721
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064219|gb|FL094756.1|FL094756
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCCACTGATATGGAGGCTCTGAAGTCCCCTTTGAT
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCC-ACTGATATGGAGGCTCTGAAGTCCCCTTTGAT
EST: gi|32938598|gb|CF043417.1|CF043417
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|30087663|gb|CB885869.1|CB885869
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|33094579|gb|CF054573.1|CF054573
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064213|gb|FL094750.1|FL094750
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAAGTCC
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAA-GTCC
EST: gi|149098467|gb|EE184446.2|EE184446
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|32939909|gb|CF044728.1|CF044728
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211066964|gb|FL094768.1|FL094768
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGAT
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGAT
EST: gi|32932660|gb|CF037472.1|CF037472
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|149103159|gb|EE288530.2|EE288530
EST:     ACTTGTCATTCCAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064225|gb|FL094762.1|FL094762
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGNAG                         ATT-ACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGT
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGT
EST: gi|211064220|gb|FL094757.1|FL094757
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064224|gb|FL094761.1|FL094761
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGGCTCTGAAGTCCCCT
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGG-CTCTGAAGTCCCCT
EST: gi|211064214|gb|FL094751.1|FL094751
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCC
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCC
EST: gi|211064212|gb|FL094749.1|FL094749
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|32932658|gb|CF037470.1|CF037470
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211066962|gb|FL094766.1|FL094766
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGA
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGA
EST: gi|211064215|gb|FL094752.1|FL094752
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATTGGAGGCTCTGAAGTCCC-TTTGA
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATAT-GGAGGCTCTGAAGTCCCCTTTGA
EST: gi|33104315|gb|CF064275.1|CF064275
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
EST: gi|211064217|gb|FL094754.1|FL094754
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCTGCCACTGATATGGA
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGA
EST: gi|32939179|gb|CF043998.1|CF043998
EST:     ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAG                         ATTTACAAGGTCCCCGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG
genomic: ACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATG

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: 498

GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATGGGTCTATTCGAGAAGCGCAGAGCAAGGAACTTCTTCATTTATGTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 517

GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATGGGTCTATTCGAGAAGCGCAGAGCAAGGAACTTCTTCATTTATGTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 574

GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATGGGTCTATTCGAGAAGCGCAGAGCAAGGAACTTCTTCATTTATGTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcacca ... attcaatcagATTTACAAGGTCCCTGCCACTGATATGGAGGCTCTGAAGTCCCCTTTGATGGGTCTATTCGAGAAGCGCAGAGCAAGGAACTTCTTCATTTATGTCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAATGGGACATTGGTTCGAACCCTCATCCACACTGATGTGACAAAGTACTTGTCATTCAAAGCTGTTGATGGGAGCTATGTTTTCAGCAAAGGGAAGgtagtcaccagtctatgttcttgttcttttttttcatcaacatcgcgtttcctgaattttcttatatcaggtagggtaacataccttgtctcttttattatattcaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG