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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag

Basic information

species Zea mays
transcript GRMZM2G028089_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag
||||||||||| |||||||||||||| || |||||||||||||||||||||||||||||||| || || || ||||| ||| ||  |||| |||   | |  | | |          |||  | |     | |||  | |||      ||| |||   || ||    | ||| |  | ||  |||||     |                                
ACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAATgtgagggttcttcttatcatcagtttat-------gtcttacagatattgagttgtactacccaatatattgtttttggaaaaa----tgatactgacagatatatttgagcag--------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag
||||| || || ||  ||||||| || || |||||||| ||||| || |||||||||||||||||||| || || || ||| ||  || |  | |  |  | ||| |     ||   ||||   ||| |  |   |||    ||||      ||| |  |    |  || |||| |   ||||| || |                                    
ACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtgagtgtttt--tctagactcttcttt----gcattattatctttcattaagc--ctttggagtgggggaagtttttttatttctgttcttattgtt--aggtaattat------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag
||||| || || ||  | ||||| || || |||||||| ||||| || |||||||||||||||||||| || || || ||||||  || | ||   |  | ||   |   |  | || | |           | |||| |     || ||           || |  |  |  | || |   |  || || ||                                
ACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtaagtgtttttct---agactcttctttgcattatatctttat---------tatctttcattaagcctttggagtaggggaagtgtt--tgatttctgttctgattgtcagg--------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag
|| || || ||||| || |||||||| || |||||||| ||||| || ||||||||||| || ||||| || |||||||||||||  | || | | |         ||| |   |   ||    || ||   |   ||  |    || | |  || |      ||      ||| |  |  |                                           
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagc--tttattatca-------cttcatatttatcata---atctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcag-------------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag
|| || || |||||  ||||||| || || |||||||| ||||| ||||||||||| || || ||||||||||| |||||| ||| || |      ||  | | ||  |   | | ||  || |||  |   ||| ||   | ||  | | | |||  |   |                                                              
ACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagccttatgtcactaatacatatcatact-ccacttcctgagtc--ttactgtttttggc-tgattattcgttcatatgcag-------------------------------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcatt-----ctac-----tttgaagccctctctcaaaacaaatttatggg---tcagtgggtgtcttccccgtggctttg--ctttctcaacaaatagt-catattatccgaggtat----ttttctggatagaaatgtactaaacgatgcttttgtgcag
|| ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| ||||| || |||||||| |||||||  |     | ||     |||   | | | ||||  | ||  |||   |    | |     |   |   | |  | |||   | || |||| | ||| |    ||| |   | | |     | || || || |   |  |      | |   |||||||||
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag

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|5343228|gb|AI795413.1|AI795413
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|74245516|gb|DT653430.1|DT653430
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|37383993|gb|CF629039.1|CF629039
EST:     CAGCAGCAACTCAGT                         TGGCTGCTCATC-TACAGGGAATACACAGTGCCATCAAGATGCTCAATAGC
genomic: CAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACA-GGAATACACAGTGCCATCAAGATGCTCAATAGC
EST: gi|37378561|gb|CF625975.1|CF625975
EST:     CCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGATGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|148964739|gb|EC906002.2|EC906002
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGGATACACAGTGCCATCAAGATGCT
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCT
EST: gi|71427075|gb|DR808125.1|DR808125
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTT
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTT
EST: gi|78079914|gb|DV508326.1|DV508326
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGGCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|71428766|gb|DR809816.1|DR809816
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|71428767|gb|DR809817.1|DR809817
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGNTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGA
EST: gi|78079913|gb|DV508325.1|DV508325
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|5847033|gb|AW000112.1|AW000112
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACNCAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|78104235|gb|DV522653.1|DV522653
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|5650012|gb|AI920372.1|AI920372
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|76925807|gb|DV170603.1|DV170603
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
EST: gi|74245515|gb|DT653429.1|DT653429
EST:     CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT                         TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA
genomic: CCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCA

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: 106

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 44

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 36

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattc ... ttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG