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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagtttctgggttgtaaccaattgtcttcttcgattgcgttgtag

Basic information

species Zea mays
transcript GRMZM2G050371_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 5'ss of exon 3
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagtttctgggttgtaaccaattgtcttcttcgattgcgttgtag
||||||||||||||| || || ||||| ||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||       || | | |  ||  |      ||    | |||| |||  ||  |   || | || |||| ||  |||  ||||   || ||
ACCTGTCATAAATGGCCTTACGGACTACAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTCGAACACATTGGTCGTATTGAAAACACTAAGgtagat------catttattgcaccctaaggaaccaccatgtaatcttgctttagtatattatgactaattttcaacttttattgttatgaag

upper sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G03360.1 (Glycine max), 5'ss of exon 3
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagt----ttct-----gggttgtaacc-aattgtcttcttcgattgcgttgtag-
 || ||||| |||||  | || ||||| |||||||| |||||||||||||||||||| ||||| ||| ||||||| || |||||  |||||   || |||||    | ||     |    |    |  ||| || | |  ||||||    ||    |||      | |||||   |  | ||| |||| | ||     |||   
GCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGGTTGAGCACATAGGTCGGTTTGAAGGTACAAAGgtcaggttatgttgtttgtcttgaag-attttgcttcttcctaattcgtggtggcattcgtaagggagttgttgtctgactgttttctgcaatacaaatgtcag

upper sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G03280.1 (Glycine max), 5'ss of exon 3
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagtttctgggtt--gtaaccaattgtcttcttcgatt--gcgttgtag-------
 || ||||| |||||  | || ||||| |||||||| |||||||||||||||||||| ||||| ||| ||||||| ||||||||  |||||   || |||||    | ||    ||    |      ||||| | | |  |||||| |  ||  |    |   |  |  | |||||||  |  |||  || ||  |        
GCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGGTTGAGCACATTGGTCGGTTTGAAGGTACAAAGgtcaggttatgttgcttgtcttgaaaagtttg-cttcttcctaattcttggtggcattttcaagggaatagttgtcttactgtattctgcattacacatgtcag

upper sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataaca--ctgaattaac------tgtgtttggcct----gtgtctaattt-tgagtttctgggttgtaa--ccaatt--gtcttcttcgattgcgttgtag--------
||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || ||  |||| || |||||||   | |||   ||||||||   |  ||      |||  | ||       ||| |||| ||     |  |||  ||  | || |  |  |||| ||  | | |    |||  |  |||  |  |||          
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag

upper sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S189_99V6.1 (Physcomitrella patens), 5'ss of exon 8
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgt----ttggcctgtgtctaattttgagt--ttctgggttgtaaccaattgtcttcttcgattgcgttgtag-
 || ||||| ||||| || |||||||||||||| || |||||||| |||||||| |  || |||||   ||||   |||||   ||| ||       ||||||           | |||||  ||   |     |  | ||||   | ||   |||  |  | |   ||      |||  || | || ||  |||     
TCCCGTCATCAATGGACTTACTGACTATAACCACCCTTGCCAGATCATGGCTGACGTCCTAACTATTAATGAGTTCATTGGCAATATAGAGGGTCTGAAGgtatgccttgctttcggaattcgctacatagtgctatcttgtgataagttgacagtggtattcgtcggtggttttttggtttttacgttttggttaactt

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|60341228|gb|DN208201.1|DN208201
EST:     GTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: GTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|116817077|gb|EC859881.1|EC859881
EST:     -GATGCACTTACTATGCTATGAGCAGATTGGTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: TGATGCACTTACTATGCT-TGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|94473220|gb|EB702178.1|EB702178
EST:     CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|78077353|gb|DV505787.1|DV505787
EST:     CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|78125153|gb|DV543537.1|DV543537
EST:     CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|149072339|gb|EE160609.2|EE160609
EST:     AAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: AAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
EST: gi|60394172|gb|DN227042.1|DN227042
EST:     CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAG                         GTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG
genomic: CTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTG

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), 45 (downstream exon)
Score: 180

ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGCTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 222

ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGCTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 123

ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGCTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat ... tgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGCTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagtttctgggttgtaaccaattgtcttcttcgattgcgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT