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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaacacgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcag

Basic information

species Zea mays
transcript GRMZM2G107101_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g08700.2 (Oryza sativa), 5'ss of exon 14
TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaaca--cgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcag
 ||||| |||||||| || |||||||| || || ||||| ||||| || || ||||||||||| || |||||||||||||||||||| |||||  | ||||| |||   | | ||||| | || |    ||   | | |   |    || || | ||  |  |   ||  || || |    |  | | | | |     |||  |  | || || |  |||                                           
AGAAGCATTGGTGATCCTTGCTAGTGCTTCAGATCTTCTTCTTCGAGCAACTGATGGAATGCTTGTTGATGGTGAAGCTTGTACTTTACCACAATTAGAGgtaaca---ccttcattcatgaggtcct-taggtgcaaatcccagtgaagaataatcagttctactttgtatggttcatctcgcttactgaccggttcatctcgggatcaattacgagcag------------------------------------------

upper sequence: GRMZM2G107101_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 5'ss of exon 12
TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgt-cattaaacacgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcag
|||  |  ||||||| ||||| ||||| || || ||||| || || || || ||||||||||| || ||||| ||||||||||| || || || |||||||| ||    ||   ||     ||||| |    ||      ||||||   | | | |     |  | |||   |    ||  ||||   ||||||     ||                                                             
TGAGTCACTGGTGATTCTCGCAAGTGCATCAGATCTTCTTCTGCGGGCAACTGATGGAATGCTTGTTGATGGAGAAGCTTGTACATTACCTCAACTTGAGgt-actgcactgttat-----agattgctcttcaatgcccttcttcgggctagagtaataatcattttctgat----tccactgtattttaaacttttgcag------------------------------------------------------------
















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|13315954|gb|BG410302.1|BG410302
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAG-GACCGCTCGGGCTG
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTG
EST: gi|91873510|gb|EB403467.1|EB403467
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|78180470|gb|DV550843.1|DV550843
EST:     CTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|16921389|gb|BM075127.1|BM075127
EST:     GCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: GCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|8516555|gb|BE123280.1|BE123280
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211222361|gb|FL433496.1|FL433496
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|18173100|gb|BM348488.1|BM348488
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGAAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGNAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211125421|gb|FL376738.1|FL376738
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|18170800|gb|BM340640.1|BM340640
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|18176877|gb|BM351810.1|BM351810
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|60352308|gb|DN219281.1|DN219281
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|67013730|gb|CO442479.1|CO442479
EST:     CCGATGGAATGCTCGTNGATGGTGAAGCTTGTCCTTTGCCACAGCTTGAG                         CTCCTGGAA-TGACCGCTCGGGCTGTCC
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCC
EST: gi|60349242|gb|DN216215.1|DN216215
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|6827225|gb|AW330868.1|AW330868
EST:     CGATGGAATGCTCG-CGATGGTGAAGCTTG-ACTNTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CGATGGAATGCTCGTCGATGGTGAAGCTTGTACT-TTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|93283882|gb|EB676146.1|EB676146
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|18174631|gb|BM350019.1|BM350019
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|28986264|gb|CB351049.1|CB351049
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|13490512|gb|BG517276.1|BG517276
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|113701581|gb|EE679085.1|EE679085
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|116818296|gb|EC861304.1|EC861304
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|12046987|gb|BF729126.1|BF729126
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|113703434|gb|EE680938.1|EE680938
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211306980|gb|FL381266.1|FL381266
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211167624|gb|FL375018.1|FL375018
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTC-ATCTTACCATCGAATGGGGAGA
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGA
EST: gi|211533313|gb|FL400718.1|FL400718
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211444132|gb|FL303929.1|FL303929
EST:     GTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: GTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|17929970|gb|BM266924.1|BM266924
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|32845254|gb|CD984935.1|CD984935
EST:     ACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: ACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|18165061|gb|BM334906.1|BM334906
EST:     AGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: AGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|8103030|gb|AW927697.1|AW927697
EST:     GCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: GCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|30087797|gb|CB886003.1|CB886003
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATTTTTTAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT

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: 329

TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 298

TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCGTTGGTGATACTCGCTAGTGCCTCCGACCTTCTACTTCGTGCTACCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaacacgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC