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'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattgttttggttctttctagcttccagcctgctttcatggcgatactttacctttcatgtgcagaagtcaataatagacactcaaataccatatctgttcgtaacaagatcagcagctgttcacatacaaagtgttgctttttctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG

Basic information

species Zea mays
transcript GRMZM5G807639_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 7
gtgaattgttttggttctttctagcttccagcctgctttcatggcgatactttacctttcatgtgcagaagtcaataatagacactcaaataccatatctgttcgtaacaagatcagcagctgttcacatacaaagtgttgctttt-tctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG
                                                                           | | | ||| | |  | |   |  ||   |         || ||  | |||||    ||  | ||  |||  ||   |  | |||| ||| |||||||||| ||||| || || |||||||||||||| |||||||| |||||||| ||||||||   ||| |||||||||||||||||||| |||||||
--------------------------------------------------------------------------gtgaaaaacattgaccttctcaacttggctgctttcg--ccatcatat-ttcactccgaagctatttttttgatcgtgccttggtttccagTTCATTGCTAGCGAAGGTGATACTGTTACTCCAGGCACCAAAGTTGCTATCATATCAAAGTCTGCGGCACCAGCTGAAACACATGTTGCTCCGTCTGAGG
















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|211511665|gb|FL408091.1|FL408091
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGT-GCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211042919|gb|FL416910.1|FL416910
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         TTCTTTGCTAGTGAAGGGGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211150258|gb|FL395029.1|FL395029
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211479894|gb|FL423794.1|FL423794
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAAT
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAAT
EST: gi|67025111|gb|CO453860.1|CO453860
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211461966|gb|FL427684.1|FL427684
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCNNTG-TGT-ATTGAAAAG                         CTCATTGCTAGTGAANGCGACACANGT-ACTCCAGGGACTAAAGTTGCAAT
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGC--TGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACA-GTTACTCCAGGCACTAAAGTTGCAAT
EST: gi|32862756|gb|CF002438.1|CF002438
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAA
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAA
EST: gi|30306817|gb|CD001490.1|CD001490
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211518170|gb|FL380292.1|FL380292
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211490936|gb|FL402016.1|FL402016
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACAC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACAC
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|28187901|gb|CB179511.1|CB179511
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGGCACTAAAGTTGCAAT
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGG-CACTAAAGTTGCAAT
EST: gi|211437186|gb|FL418966.1|FL418966
EST:     GTCACTATAGATGTCGCAAGTTCCTGAAGCTGGTGTTATTGAATAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGG
genomic: GTCACTATAGATGTCGCAAGT-CCTGAAGCTGGTGTTATTGAA-AAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGG
EST: gi|37420219|gb|CF647798.1|CF647798
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGCTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|93017175|gb|EB642695.1|EB642695
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211305586|gb|FL419218.1|FL419218
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211142865|gb|FL377125.1|FL377125
EST:     -TCCACTATAGATGTCGCAAGTCCTGGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAG
genomic: GTC-ACTATAGATGTCGCAAGTCCTG-AAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAG
EST: gi|211530093|gb|FL390761.1|FL390761
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCCGGCACTAAAGTTGGCA-T
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTG-CAAT
EST: gi|211235901|gb|FL373720.1|FL373720
EST:     GTCACTATAGATGTCGCAANGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCA
genomic: GTCACTATAGATGTCGCAA-GTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCA
EST: gi|211063833|gb|FL423073.1|FL423073
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211441962|gb|FL416333.1|FL416333
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCG
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCG
EST: gi|32834807|gb|CD974485.1|CD974485
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211094733|gb|FL379398.1|FL379398
EST:     GTCACTATAGATGTCGCAANGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAA-GTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|211539307|gb|FL400264.1|FL400264
EST:     GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACT
genomic: GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACT

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: 45 (upstream exon), 49 (downstream exon)
Score: 203

GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 420

GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 376

GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 411

GTCACTATAGATGTCGCAAGTCCTGAAGCTGGTGTTATTGAAAAGgtgaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatcagcagctgttcacatacaaagtgttgctttttctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCTGAGG
                                    ttctgac  putative branch site (score: 411)
                   atacaaa  TA-rich tract