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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttctgggactgggatcatagtatactattggccctttttattgtatttttgtgtatatatatgatatgaaactcaagtgcgtgcacttgcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 3'ss of exon 7
atttctgggactgggatcatagtatactattggccctttttattgtatttttgtgtatatatat-gatatgaaactcaagtgcgtgcacttgcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG
 | |    |||   | |||| |  | |      ||     ||  ||   | ||    |   |||  || ||||||||||||   |||| |   |||||||||| ||||||||||| |||||||||||||||||||||||||| || || ||||| || |||||||||||| |||||||   |||||
ttgtgaatgaccaag-tcatggatttcctagaaccagggataccgtgcatctgctccttgctatcaatgtgaaactcaagtatctgcattgttttttgcagTATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAG
















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|74235678|gb|DT643592.1|DT643592
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|4804174|gb|AI666040.1|AI666040
EST:     GTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|166563741|gb|EG244809.1|EG244809
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCC
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCC
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 64

GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 62

GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 74

GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 88

GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttgtgtatatatatgatatgaaactcaagtgcgtgcacttgcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG
                                          cttgctttt  CT-rich tract
          tatatatatgatatga  TA-rich tract