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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgcctggcggtggtgcctgtatcttccccttccacgcacgctgcttaaacgcgtttttttttcgctccacgcggagccgcttgcttgcttgcg...

Basic information

species Zea mays
transcript GRMZM2G079682_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079682_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g38160.1 (Oryza sativa), 5'ss of exon 1
GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGC---TACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgcctggcggtggtgcctgtatcttccccttccacgcacgctgcttaaacgcgtttttttttcgctccacgcggagc-cgcttgcttgcttgcg-------
 |     ||  | || |     |  | ||| |  ||||||||||||   |||| |||| |||||||||| |||||||||||||| | ||||||||||||||||||||| | ||| |||     | |||    || | |||||| | ||  | | |    ||| ||   |   ||| || || |   | | ||  || |    ||       
CTTCTTCGCCGCCGCCG-CCGCCGCCGCGGGG--ATGGAGGCCGGCGGGTACTACAACTGCAAGAAGACGGACGGCATCTGCGAGGACGTCTGCGACAGCGAGgtgag-cggcccggc-----tccctcctcctcctccttccgc-cat-cagatctgtcgctttcactccccgcgccgcgtgtttctctctctctcgaacccgttcttga
















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|148989949|gb|EE031822.2|EE031822
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71432765|gb|DR813815.1|DR813815
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|50328019|gb|CO523145.1|CO523145
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|149105738|gb|EE291314.2|EE291314
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71430357|gb|DR811407.1|DR811407
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|148931731|gb|EC874964.2|EC874964
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71312923|gb|DR792984.1|DR792984
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|148957087|gb|EC903057.2|EC903057
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|149098671|gb|EE184680.2|EE184680
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|78086273|gb|DV514666.1|DV514666
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71447556|gb|DR828606.1|DR828606
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|86466341|gb|DY232712.1|DY232712
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71767841|gb|DR965778.1|DR965778
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|78078055|gb|DV506470.1|DV506470
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-A-                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|76926193|gb|DV170756.1|DV170756
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71770961|gb|DR968898.1|DR968898
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71449434|gb|DR830484.1|DR830484
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|149102165|gb|EE287589.2|EE287589
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|149105856|gb|EE291458.2|EE291458
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|78106713|gb|DV525131.1|DV525131
EST:     GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAG                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: GCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG

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), 46 (downstream exon)
Score: 30

GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 88

GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 46

GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgc ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTGCTCCTGCTGATTTTCTTCTCGGCGCCATGGAGGCCGGCTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGAGgtgaggccgcctggcggtggtgcctgtatcttccccttccacgcacgctgcttaaacgcgtttttttttcgctccacgcggagccgcttgcttgcttgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttcc