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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgtactaatcgatgatttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG

Basic information

species Zea mays
transcript GRMZM2G080652_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 5
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgtactaatcgatgatttcgtg---cagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                                       ||  | ||  |    |  | |  |||   |  |     ||||||  |  | | |   || |  || |    |    | || || || ||| |||| |    ||||||||||||| ||||| || | ||||||||||||||| |||||  |||||||  |    ||  | || || |||||  |||| ||||||||||
-------------------------------------aatgttgttgattgatgtaagtcactgca--cctagtgggattagttgtgatttttttagttttattttatgta----tctaatattccatgttttcttattacagTGGCTGCTCACCTTACTGGTACACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACACCACTATCTTCTTGCAATGCAAAAAG

upper sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcata--ctgtctgaggtatatttctggacagaattgtactaatcgatgatttc---gtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                                       ||  | | |  | | |||   |       |  |      | ||   |    | | | || | ||||      ||    | || || || ||| ||||    ||||||||||||||| ||||| |||||||||||||||||||| |||||  |||||||  |    ||  | ||||| |||||  |||| ||||||||||
---------------------------------------tgttgat-tgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtatt-----gcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG

upper sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgta---ctaatcgatgatttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                                           |    |||   | |  |||    ||      || || |    | || |||    | |   |||| |  ||||| ||     | ||   ||||| |||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||  || | ||  |  | ||| || | || || ||||| ||||
-------------------------------------------gtaagctttattatcacttcatattt-----atcataatctgttctttct----ttttcatctgcatggaattttaggttgattcctcgattttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG

upper sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgtactaatcgatgattt-cgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                                                       |||    |  | | |||  | ||    |||||||        |   | |    || |  ||   || ||   |  ||    ||||||||||||||||||||| || ||||| ||||||||||||||||| ||||||||  || | ||  |  | ||  |||| | ||| ||||| ||||
-------------------------------------------------------gtgagcct--tatgtcactaatacatatcatactccacttcctgagtctt---actgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG

upper sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 5
----------------------gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttg-ctttctcaacat-tattagtcatactgtctgaggtata--tttctggacagaattgtactaatcgatgatttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                       |      | |  | |     ||| |    ||| |    |      ||  | |    |  |||  | || |||| |  |||||  |||  | |       | |   || || |  |  ||  |    | | |   || ||||||||||||| || || || || ||||| ||||||||||||||||| ||||||||  |||||||| | ||||| |||||  |||| ||||||||||
gtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCAGAATCCGTGTTCTTCATCATTATCTGCTTGCTATGCAAAAAG

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|211040785|gb|FL108285.1|FL108285
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|32823725|gb|CD963447.1|CD963447
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|31360794|gb|CD445151.1|CD445151
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCT
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCT
EST: gi|78117501|gb|DV535888.1|DV535888
EST:     CCATGTTGCCCATCTCTAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|71330852|gb|DR802224.1|DR802224
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|32823775|gb|CD963497.1|CD963497
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|76294373|gb|DV033941.1|DV033941
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGGTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|71309452|gb|DR791013.1|DR791013
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|24768059|gb|CA403191.1|CA403191
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|78117500|gb|DV535887.1|DV535887
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|71330843|gb|DR802223.1|DR802223
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|101386958|gb|EB815496.1|EB815496
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAA
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA

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), 47 (downstream exon)
Score: 51

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 48

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGTgtaagagtta ... tttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgtctgaggtatatttctggacagaattgtactaatcgatgatttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG
                                tactaat  putative branch site (score: 57)
            tatatttct  TA-rich tract