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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag

Basic information

species Zea mays
transcript GRMZM2G056099_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g20310.4 (Oryza sativa), 5'ss of exon 8
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaac--ttttcagatacctccaaccc-tggcaaac-atttag-----ttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
||||||||||||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |||||||| || || ||||||||||| || ||||||| | ||||| | | | | | ||||| ||| | || |||| | |||| | || | ||| | || ||| ||| | | | |
CCTTGGTCCATCAGGATCTTCAGGGAACGTGGCAAACTACATGGGTCAAATGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtctttcaaaatcatgtggcatatttcaaactgtttcgaaattttctgttatctctgattctggcaagcat---gcactcttgttatt-gctgtaaca------------------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G39050.1 (Glycine max), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacatttt---ctctacttttaaga-aatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
||||| | || || || || || || |||||||| || |||||||||||||||||||||||||| ||||| || ||||| ||| ||| || |||||||||||||| | ||| | || | || || | || || || | | || | | | ||| |||| | || || | | ||| |||| | || || | ||| | || ||| | | | |||
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaacttttctta---ctcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaag-------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 5
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| | ||||||| || | ||||| |||||||| | ||||||||||| |||||||||||||||| ||||| ||||| ||| || |||| ||||||| || | || || ||| | | || | ||| || | | | | ||| || | || | | | | ||| | |
GCCCAGCTCATCAGGCTCCCCGGGAAATGTGGCAAATAACATGGGTCAAATAACTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCTCCAGgtacgctcattttccgg-tctaattctgtt---ttctcaacttccatctttttgaaataaagagaactcaggaagctttg--aattaactgagtttaatttatttg-------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G31050.2 (Glycine max), 5'ss of exon 9
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttg--attcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| | ||||||| || || ||||| ||||||| || ||||| ||||||||||||||||||||||| ||||| || || || || |||||||||||| || | || || ||| | | || | ||| || | | | | || || ||| | || ||| | ||
ACCCAGCACATCAGGCTCCTCGGGAAATGTGGCAAGTTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACTCTTGATGGGTTTCTTCGCCAGgtacgctcattttccgg-tctaattctgtt---ttctcaacttccatctttttgaaataaagagataaagagaactcaggaagcttagaattaagtgagttaaa-----------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 9
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgtt-cctagctctgaagacttttggtgttctattatcgttag
||||| | || || || || || || |||||||| || |||||||||||||||||||||||||| ||||| || ||||| ||| ||| || |||||| |||||| ||| || | | | ||||| || | | || | || | ||| ||| || | | | | | || | || | | | || || | | | |||||| | ||||| || | | | |
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGATTCATTAAGCAGgtatgcttttct--tactcacat-----gtgtgcgatcagtttggtacatatt-----------tctcaaagaaa--atgctctttcatacagcatttcatggcagattattgataacaaac----atcactattaaaataacttggctctgtttatttttgtggtcatttgaaag----

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| | ||||||| || || ||||| |||||||| || ||||| ||||||||||||||||||||||| ||||| ||||| ||| || |||| ||||||| || | || || ||| | | || | ||| || | | | | ||| || | || | | | ||| | |
GCCCAGCTCATCAGGCTCCTCGGGAAATGTGGCAAATTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcattttccgg-tctaattctgtt---ttctcaacttccatctttttgaaataaagagaactcaggaagctttg--aattatctgagtttaatttatatg-------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| || |||| || || || || || |||||||| || |||||||||||||| ||||||||||| || || || ||||| || ||| ||| |||||| ||||| | | || | | ||| |||||| | | | || | | || | | ||| || ||| | | || ||| | |||
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAATTACATGGGTCAAATGGCCATGGCCATGGGTAAGCTAGGGACACTTGAAGGGTTCATTCAACAGgtacttttttc-----tttgttgcacttgtatacaaatagttt-gctacattggtgaataagtg----aagaaga----atcttttagtccagccttgatttcctaatattatt-----------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 11
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagat-----acctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
||||| | || || || |||||||| |||||||||||||||||||||||||| |||||||||||||| || || || || ||| || |||| |||||| | || | | | | | |||| ||| | | ||| | | || | | |||| | | || || | || |
TCTTGGCTCTTCTGGTTCATCTGGAAATGTGGCAAACTATATGGGTCAAATGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttctaaagttttgattttctttcctgacaataagaataaaatcttgatcatattatggtctgtttatgatcaaccagaaagttagga--aatgga----------------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S126_196V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctc--caaccctggcaaacatttagttttgt---tgtttctgttgttgactgtcataggga-----gatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcct-agctctgaagacttttggtgttctattatcgttag
||||| | || || || | ||| || || | |||||||| || ||||| ||||||||||| |||||||||||||| || |||| | | |||||| | ||| | | || |||| | | ||||| | | | | |||| ||| || | | | |||| | || || | | | | | | || | ||| | | | || | || || | || ||| | | | | | | ||
TGTTGGTTCTCTTGGCTCATCAGCAAATGTAGCTATTTATATGGGACAGATGGCCATGGCCATGGGGAAACTTGGCACACTTGAAGCTTTCATGTGTCAGgtatatatttatattgattttgcatagctgggtgttgtatggttttttatgcggcattttggttggaagtctcgaggcatgttgcttgtatcatctagcattatgtgggttgttctcagtaatgcagtaca-gtacgctattagccttttttttcaggtcagttaacgattgttttgatggttttgacag

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 2
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
|| | ||| || ||||| || ||||| ||||| |||||||| ||||| |||||||| || || || |||||||| || |||||||||||| | | | || || || | | || |||| |
TGCCGGCTCTCTGGGAAACTCCCCCAACGTAGCGAACTACATGGGACAAATGGCCATGGCAATGGGAAAGCTCGGAACTCTCGAGAACTTTGTTCGCCAGgtaacgcgagccgcgatctttctttctcgctgataatt--ctttggcgcag--------------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ22847 (Selaginella moellendorffii), 5'ss of exon 5
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| || | || | || ||||| |||||||| ||||| || ||||||||||||||||| || || ||||| || || || || |||| |||||||| || | | | | | ||||| ||| || || | ||| |||| || | | | || || ||| || |
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaa---gccaaactctttcttcttcttttttcatttccagcagtttttcttggtcttgctctccataatgaaagt-tctgccttagttttccacagcttttt---------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ28227 (Selaginella moellendorffii), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
||| | | || || | || || || ||||||||||| |||||||| ||||| |||||||| || || || |||||||| || |||||||||| | | | | || || | | || || | || || |
GACTGGCTCCTTGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTTGTTCGCCAGgtga---tgtgatgtatctgtggtttca-cgattgtt--gtctcaactttccttctaccag----------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ30797 (Selaginella moellendorffii), 5'ss of exon 6
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
| || | || | || ||||| |||||||| ||||| || ||||||||||||||||| || || ||||| || || || || |||| |||||||| || | | | | | | ||| ||| || || | ||| |||| || | | | || || ||| || |
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaa---gccaaactctttcttcttcttttctcttttccagcagtttttcttggtcttgctctccataatgaaagttttgc-cttagttttccacagcttttt---------------------------------------------------------------------------

upper sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ29724 (Selaginella moellendorffii), 5'ss of exon 7
CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttag
||| | | || || | || || || ||||||||||| |||||||| ||||| |||||||| || || || |||||||| || |||||||||| | | | | || || || | | | | || || |
GACTGGCTCCTTGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTTGTTCGCCAGgtga---tgtgatgtatctgtggtttcacca---ttgttatctcaactttccttctaccag----------------------------------------------------------------------------------------------------------------------

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|32801942|gb|CD954178.1|CD954178
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAG                         GCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
EST: gi|32794757|gb|CD946993.1|CD946993
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAG                         GCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
EST: gi|32824133|gb|CD963855.1|CD963855
EST:     GGCTATGGCCATGGGAAAACTTGGCACACCTCGAGAATTTCCTTCGCCAG                         GCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: GGCTATGGCCATGGGAAAACTTGGCACA-CTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
EST: gi|50323432|gb|CO518558.1|CO518558
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAG                         GATGACAATCTTCGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
EST: gi|67014815|gb|CO443564.1|CO443564
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAG                         GCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
EST: gi|78116763|gb|DV535150.1|DV535150
EST:     TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAG                         GCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA
genomic: TGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACA

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

CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 154

CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 131

CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

CCTTGGTCCATCAGGATCTTCTGGAAACGTGGCAAACTATATGGGTCAAATGGCTATGGCCATGGGAAAACTTGGCACACTCGAGAATTTCCTTCGCCAGgtaaactttt ... ttatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC