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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT

Basic information

species Zea mays
transcript GRMZM2G095593_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
|| |||| || || ||||     ||   |   ||   ||||| ||||| ||  | |    ||||||||   ||||      ||||            | || |   ||||| |||     ||   ||| |   || | |  |  |  ||  |   ||  || ||| |||||| |  ||||  ||||||||||||| || || ||||| || ||||||||||||||||| || ||||| |||||||||||||| ||||| ||||||||||| |||||||| ||| |||
gttagtgttctggtttgcg----tattgggagtc---aatatagctta-tggcagtaatgcaggcttcagccctc-----catttatg---------gcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgca-ttgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttc---tgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                                                                 ||   | | |  || |||  |  |   ||     ||||| || | ||   |  |   | || | ||||   |       |||  ||| |  ||||  |||    | |||||||| || || |||||||| || || || ||||||||||| ||||||||| | || ||||| ||| | || |||||||| ||||| || || ||| | |
--------------------------------------------------------------------------------gatccacatctcactgtgtcaactttgttt-----ttattattgtgtatcgtgta--ctacacacagcaca-atcaatttagt--ctaatacaaacccttttactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaat-attgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                | |||  | ||   ||  |  |  | |  | |  ||            | || | | |||  |||| |||||||   ||  ||| | |||   | ||      ||| ||     ||||| |  |  | |  || ||  |       || | | |||||||| || || |||||||| || || |||||||||||||| ||||||||||| || ||||||||| | || ||||| || || || || |||||| | |
-------------------------------gtttgtgtttatcttttgcttcttctagagctgttttaatagagtttcaacatctcctttttactatctttatct---tttggcagtgtttcaatttaag---gagtgttt---cagcatct--taagactatgcctttt-------gtgtattcagGCTGTGGCAAACTCAACATCAGCAACATTCTTGCGTGTTGTTGGTAGTGAACTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTAAGAGAACTTT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                                                                 ||      ||| |  |||   |||   | |||  |     | || | ||    |  ||   ||  |  || |  || |||     || ||     | ||  | ||||| || || ||||| || || || ||||||||||||||||||||||||||||| ||||| |||||  | || |||||||||||||| || || ||| | |
---------------------------------------------------------------------------------atggattgttg-cagtgtgcctctttttaatgtgt----ctcttatgcttgttaaattcggaactgt-tggagatgagcaagtgttatttcttgttattctttcagGCAGTGGCAAATTCTACTTCAGCTACTTTCTTGCGTGTTGTCGGTAGTGAACTGATTCAGAAGTATTTAGGAGATGGTCCCAAGCTTGTGAGGGAACTTT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                                                                | | | ||||| ||  | | | ||||    | |||| |  |  ||  | | |   | | | |  ||    | |   |  |  | |||   |||   | |||    |||| ||||| ||||||||||| || ||||||||| | ||||| |||||||| || ||||| |||||  | || |||||||| ||||| || |||||| | |
--------------------------------------------------------------------------------tgtcttcctttctc-gtttctctctgtcacaagcatgagatagttgcaatttggtggtgttatctaatgggaataagctctctaact---tgatcttatttt---agGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                                                                                                            |        ||  ||| ||   ||   | |||     || ||||  |     || |||| ||||||||||| || || |||||||| || |||||||||||||| || || || ||||||||||||||  | || || ||||| ||||| || || ||  | |
---------------------------------------------------------------------------------------------------------------------------gtaagtgtgacatcttttaaggtgc---tgcttc----gtaactaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

upper sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                                                                                                            |  |     ||  ||| ||   ||   ||||| |  | | ||||  |     || |||| ||||||||||| || || |||||||| || |||||||||||||| || || || ||||||||||||||  | || || ||||| ||||| || || ||  | |
---------------------------------------------------------------------------------------------------------------------------gtaaatgtgacatctttgaaggtgc---tacttcgtaattaactagct----ttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

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|211042217|gb|FL387609.1|FL387609
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         SCTGTTGCCAATTCAACATCTGCSACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|32938600|gb|CF043419.1|CF043419
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|116816022|gb|EC858722.1|EC858722
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|37419302|gb|CF647331.1|CF647331
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|19272515|gb|BM888771.1|BM888771
EST:     AGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCATACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: AGTCATATTATATGGCGAACCTGGAACTGGAAAAACTC-TACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|32941761|gb|CF046580.1|CF046580
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|32836748|gb|CD976426.1|CD976426
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
EST: gi|78119973|gb|DV538357.1|DV538357
EST:     GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAG                         GCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA
genomic: GAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAA

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), 48 (downstream exon)
Score: 492

CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 456

CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 569

CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctc ... gtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT
                                           ctgtttct  CT-rich tract
     tttcaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT