Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttgtcaagtgcttcagtggttttttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttg-tcaagtgcttcagtggttttttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                         |  ||||| | |  |  ||  |||  | | | | ||   ||  ||  || | | | | |  ||||  | ||||| |  |||  || ||     || |    | | | ||    |||    |   ||||||||||||| ||||| |||||||||||||| ||||||||  |||| ||||||||||||||||| |||
----------------------gtaaatttaattccaa-gttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattga--agtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

upper sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttgtcaagtgcttcagtggttttttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
              ||   || ||   |    |  | ||      |||      | |  | | ||  | | ||           | ||||      || | |||| ||||      |  |||  |  |   | ||||       | | ||||||| ||||| ||||| |||||||||||||| ||||||||  |||| || |||||||||||||| |||
--------------gtaacgtatcctcgcagtttattttaacactaatctttcgttatttacagttttcccatgatgtgtatctgcgattttttcattctgaagtacttc------tcgttatgctgaagagattgc------gtggttgcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaat-actattggacacgatggggattgacattttgtcaagtgcttcagtggttttttacccatat-atgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                                                || |   |||  | | |  | || |||   |          ||| |||| |||  |    |  |   | ||  ||   |  | ||  | | | | ||  || |  |||| || |||||||| || || || |||||||| |||||  |||| |||||||||||||||||||||
-----------------------------------------------gtgaggaagacggtttctgttgacgatttttcgtatgcattgttgccattctgttta-caatcaaccagcttcctatagacctgatagtcgatcattgggtgtt--agATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG

upper sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttgtcaagtgcttcagtggtttt-ttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                                                                                                       |||  ||  | || |  | |  | ||  || |  |   |  |      |||||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||
-------------------------------------------------------------------------------------------------------gtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

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|67025945|gb|CO454694.1|CO454694
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|71761092|gb|DR959029.1|DR959029
EST:     TGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: TGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|6095381|gb|AW120048.1|AW120048
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|149085357|gb|EE174864.2|EE174864
EST:     TTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: TTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|32839753|gb|CD979434.1|CD979434
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|32925412|gb|CF030224.1|CF030224
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|7216891|gb|AW563013.1|AW563013
EST:     TCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: TCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|71446426|gb|DR827476.1|DR827476
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|110941068|gb|EE161225.1|EE161225
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|14203981|gb|BG837658.1|BG837658
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|60340774|gb|DN207747.1|DN207747
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|30706066|gb|CD059017.1|CD059017
EST:     TCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: TCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|71446427|gb|DR827477.1|DR827477
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|7135281|gb|AW498007.1|AW498007
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|19436338|gb|BM952748.1|BM952748
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
EST: gi|6095382|gb|AW120049.1|AW120049
EST:     ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG                         ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT
genomic: ATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTT

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: 238

GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 387

GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 239

GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacac ... attgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaagtgcttcagtggttttttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG
                           atatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttgtcaagtgcttcagtggttttttacccatatatgtttgctgactgattgctgcagATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG