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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttccaagaatccagtgggtgtgtatttgcaaggctgcttgagagtagtttaacttattcttgcactccctccctcctggcag

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttccaagaatccagtgggtgtgtatttgcaaggctgcttgagagtagtttaacttattcttgcactccctccctcctggcag
|||||||||||||||||| ||||| ||||| |||||| ||||||| |||||||||||||||||||| |||||| | || || ||||||||||||||||||||||||||||| | |      |   ||| || ||   |       ||    ||||  |||||  |||   | |    |   |   |   
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagt--aactttatctgttatttatgcttgctcag---
















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|22491259|gb|BU051182.1|BU051182
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|33102735|gb|CF062695.1|CF062695
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|211465903|gb|FL134195.1|FL134195
EST:     TCATGATTGGTCCTGGGACA-GGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|211465904|gb|FL134196.1|FL134196
EST:     TCATGATTGGTCCTGGGACA-GGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|32943853|gb|CF048672.1|CF048672
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|15499663|gb|BI596176.1|BI596176
EST:     CTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGG-TAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: CTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|67026638|gb|CO455387.1|CO455387
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|32929783|gb|CF034595.1|CF034595
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GANAGGTTAGCATTGAAACAATC
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATC
EST: gi|15632677|gb|BI679770.1|BI679770
EST:     TGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|211465906|gb|FL134198.1|FL134198
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|32835080|gb|CD974758.1|CD974758
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|19437266|gb|BM953676.1|BM953676
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAG                         GAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTT

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: 510

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 605

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 692

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 746

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttc ... ctcctggcagGAAAGGTTAGCATTGAAACAATCTGGGGCAGAATTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG