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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG

Basic information

species Zea mays
transcript GRMZM2G105539_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 5
gtaataaccctaccattgtgtatcaaatgttgaatctacatg-ggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG
||||  | ||||    |||| ||| |   |||| || | | |   | ||||||||| | |||| ||| |    | || |  |||||||||||||||||| ||||||||||||||||||||| ||||||| || |||||||| |||||||||
gtaactatcctatatatgtgaatccacaattgactccatacgcacattcacattattacctatgatttgtctccctcatcaacagGGCCATACACTCCGTTTATTATCCTTGCCAGATTTCCTGGATGCATCTATTGGGAAGATCTTGAAG

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 6
----gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG
    | || ||    |   || | |||   |  |    | |   |   || ||  | ||  | | |||| |      ||  || |||||| || ||| | || ||||| ||||| || |||||||||||||| ||||||||||| ||  |||||
gtgagcaaaaagatgatagttatatatttcagatcacctttgttttttag-catttcataggat-ttatgcatg---ttacttaacagGGTCACACATTACGATTATTGTCCTTACCCGATTTCTTGGATGCATCCATTGGGAAGATACTGAAG

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG
|| |  |  ||   |||     |    |      | || || | |   | ||||  ||  |   || | || || |||  |||||| ||||| ||  || || | || || || |||||||||||||| |||||||| ||||||||||||
gtgagcaagct-tgattaaaatttcccttccctttttatattgcaaa-atattaa-agacagagtttgtta-ctactt--acagGGTCATACGCTAAGGCTACTCTCTTTACCTGATTTCTTGGATGCATCCATTGGTAAAATCTTGAAG

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 6
gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaact-tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG
||||  |    ||||   | | ||| || |    | |         ||| || |||  ||    ||  | || | || || |||||| |||||||| ||| | || ||||| ||||||||||||||||| || ||||| || || ||||||
gtaaggaaaa-accaacatatttcacatctc---tttc--------tcatatcatccactggacttgacaaattgtcattaacagGGTCATACACTGCGGCTTTTGTCCTTACCAGATTTCTTGGATGCATCTATTGGCAAGATATTGAAG

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|87153613|gb|DY398402.1|DY398402
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|148958813|gb|EC905077.2|EC905077
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|5846791|gb|AI999874.1|AI999874
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|6973389|gb|AW438083.1|AW438083
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|6031284|gb|AW076291.1|AW076291
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|5296253|gb|AI782933.1|AI782933
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|211363054|gb|FL031142.1|FL031142
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTAC-                         GGCCATACACTCCGGTTATTATCCGTTGCCAGATTTCTTGGATGCGTCCAT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCC-TTGCCAGATTTCTTGGATGCGTCCAT
EST: gi|148962847|gb|EE013769.2|EE013769
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|6973390|gb|AW438084.1|AW438084
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGNTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|18385084|gb|BM418283.1|BM418283
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGNTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|87152689|gb|DY397478.1|DY397478
EST:     CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
EST: gi|22489513|gb|BU049436.1|BU049436
EST:     CACAAGAATACAGCATGTTTAGTCTCTTTGTATTTGACACTGCCCCTACG                         GGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT
genomic: CACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATT

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: 141

GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 112

GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACGgtaataaccc ... tctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatctacatgggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG
                                     cgctaac  putative branch site (score: 123)
                                           cttcttt  CT-rich tract
                              tattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaccctaccattgtgtatcaaatgttgaatctacatgggagtcacattatcagctattattcgctaacttctttgacagGGCCATACACTCCGGTTATTATCCTTGCCAGATTTCTTGGATGCGTCCATTGGGAAAATCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG