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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattgtgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa...

Basic information

species Oryza sativa
transcript LOC_Os01g16540.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G007915_T02 (Zea mays), 5'ss of exon 2
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattgtgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa-
||||||||||||||||||| |||||||| || |||||  | |||||||| || ||||||||||| ||||||||||||||||| |||||||| ||||||||||  ||       ||  ||| | | |   |||   |                  | |  ||||||    ||      |||| |  |    |    ||    
AGCTCCTCAAGGACCTGGCTCTCTCCGGGTTTAAGAAACTGCACGTCATTGATATGGACACCATAGACGTCTCCAACCTCAATCGCCAGTTTCTCTTCAGgtccttacggtcgtctctccctacccgttccccattggcctccaagggtggattctcatctgttg-attatctggcgagatggagggagaggatagggttt

upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP05391 (Chlamydomonas reinhardtii), 5'ss of exon 1
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtt-----ttttttactctccttccttccacacgcccacctaattgtgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa
|| |||| |||||||| |||||||| ||  |   | ||||| ||||||| ||||||||||| || ||||| || ||||| |||||||| ||||| ||| |||        |    | | |   || ||    | ||         | | |||  | | | | |       |   |  |  ||   |  |  ||||    |     
AGATCCTAAAGGACCTTGCGCTCTCGGGCGTGGTGCACATCGACGTCATTGACATGGACACAATTGACGTGTCGAACCTGAACCGCCAATTCCTATTCCGgtgagcggcctcgggcgcccgagccctcagggccccgggacgggggggtcccagcactcgcgcggccacatcacactcagtcgtgtgctcccgccaccgg-----

upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S235_30V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattg---tgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa
|||| || || || ||||| || || || ||     | ||| | ||||| || ||||||||||| ||||| ||||||||||| || || ||||| ||||||||| |       || |     |   |    |      |||   ||  |    |     |   ||       |       ||  | ||  |  |||       
AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccctcatcatgtggactgaaaattctaggtgttgacttgagcattttaggatcagttgcaacttcaatttgaaagcgtatttggttgtgtaat---

upper sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ21441 (Selaginella moellendorffii), 5'ss of exon 1
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattgtgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa
|| | |||||||| || ||||||||||| ||    || ||| |||| ||||||||||| || ||||| |||||||| |||||||| || || || ||||||| | |   |    || |    ||| |||         || |     |  ||        | | | ||                                
AGATGCTCAAGGATCTTGCGCTCTCCGGCTTTGGAAATATCGACGTGATCGACATGGATACGATCGATGTCTCCAATCTCAACCGGCAATTTCTATTCAGgtgtgtgacaaaaaccat---gccaaacgagagtgagcttatatgttctttct---ttggtttcgggcag------------------------------

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|27554355|gb|CA998255.1|CA998255
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88404494|gb|CI580930.1|CI580930
EST:     GACATGGACACCATCGACGTCTCCAACCTCAAACGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|29634620|gb|CB639629.1|CB639629
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88352497|gb|CI615751.1|CI615751
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88391799|gb|CI603318.1|CI603318
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGG
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGG
EST: gi|27576209|gb|CA998903.1|CA998903
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|7168814|gb|C28508.2|C28508
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88414839|gb|CI604197.1|CI604197
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGGTGAAGTTGCTGGAAAG
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAG
EST: gi|88313796|gb|CI597427.1|CI597427
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCACTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88390471|gb|CI607507.1|CI607507
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88726387|gb|CI750042.1|CI750042
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88359773|gb|CI622463.1|CI622463
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTG
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTG
EST: gi|88360510|gb|CI608362.1|CI608362
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|58612567|gb|CK040279.1|CK040279
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|58594978|gb|CF993286.1|CF993286
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGGTGAAGTT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTT
EST: gi|88396406|gb|CI598518.1|CI598518
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|27576520|gb|CA999214.1|CA999214
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|58655476|gb|CK044156.1|CK044156
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88403087|gb|CI568861.1|CI568861
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88372622|gb|CI612550.1|CI612550
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|88391890|gb|CI603409.1|CI603409
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCCAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|58661497|gb|CK050177.1|CK050177
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
EST: gi|66915301|gb|CX102149.1|CX102149
EST:     GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAG                         GGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT
genomic: GACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTAT

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 1 RNA-Seqlibrary.


Block sizes: 68 (upstream exon), 73 (downstream exon)
Score: 24

AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgtttttttta ... tctcttacagGGTTCAAGATGTTGGGAAGTCCAAGGCTGAAGTTGCTGCAAAGAGGGTTATGGAGCGAGTTAGTGGAGTGAACATTGTTCCACATTTCTGTAGGATTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattgtgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgccg