RetrogeneDB ID: retro_rnor_390

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:257229024..257230452(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046675
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSRNOG00000037595
• Aliases: None
• Description: Vasculin-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3KR53]

Sequence

>retro_rnor_390
ATGGCGCAGCATGACTTTGTTCCTGCTTGGCTAAATTTTTCAACGCCACAGTCAGCTAAGTCATCTACAGCCACCTTTGA
CAAACACGGAGAGCACCTATCCCGTGGAGAAGGTAGATTTGGAATAAGCCGTCGTAGACATAATTCCTCTGATGGCTTTT
TTAACAATGGACCTCTGCGGACTACAGGAGATTCTTGGCACCAACCCTCCCTATTCCGCCATGATTCTGTTGACTCTGGT
GTCTCTAAGGGAGCGTATGCTGGAACCACAGGGAATCTGTCTGGTTGGCATGGCTCTTCCCGAGGTCATGATGGCATGAG
CCAACGTGGTGGAGGTAGTACAGGAAACCACCGACACTGGAATGGCAGCTTCCATTCCCGGAAAGGCTGTGCCTTTCAAG
AAAAAACACCAACTGAAATTAGGGAAGAGAAAAAAGAGGATAAAGTAGAAAAGTTGCAGTTTGAAGAGGAAGACTTCCCT
TCTTTGAATCCAGAAGCTGGCAAACAGAATCAGCCATGCAGACCTATTGGGACCCCTTCTGGAGTGTGGGAAAATCCACC
TAGTGCCAAGCAACCCTCAAAGATGCTAGTCATCAAAAAAATTTCCAAAGAGGATCCTGCTGCCACCTTTTCCGCTGCAT
TTACCTCAGGATCCCACCATGCAAATGGGAACAAAGTGTCAACCATGGTCCCGAGTGTTTATAAGAACTTGGTTCCCAAG
CCTGCACCACCTCCCTCTAAGCCCAACGCATGGAAAGCTAACAGAATGGAACACAAACCTGGATCACTTTCCTCCAGCCG
GGAGGCTGCTTTGACCAATCCAGTTTCTGTTACTAAACCAGTGGTACTAGCTGCTGGTGTAGTTCTCAACGCTCCCAAAG
AGAGTCCCTCCAGTACTACCCCTCCGATAGAGATCAGCTCCTCTCGCCTGACCAAATTGACCCGACGAACCACAGACAGG
AAGAGCGAGTTCCTGAAGACTCTGAAGGATGAGCGCAATGAAGACTGCTCCCAAAGTAGAGACTGTGACAAGCTGGAGGG
GCTAAGATTGGAGGGCAGCCACACACCTGAACCAAAGGAAAATGGAGAACAAGGTTGTCTTCAGAACGGGCTTTCTCTAC
CCATGGTAGAGGAGAGGGAGGTCCTGTCACACTCTCTAGAAGCAGAGCACAGGTTATTGAAAGCAATGGGGTGGCAGGAG
TATCCTGAAAATGATGAGAGTTGCCTCCCACTCACAGAGGATGAACTCAAGGAGTTTCACACGAGAACAGAACAGCTACG
AAGGAACGGGTTTGTAAAGAATGGCTTCTTACAAGGCCGTAGTTCCAGCCTGTTCTCCCCATGGAGAAGCACTTGCATTG
CAGAGTGTGAGGACTCAGACACGGAAACAAGCAGCAGCGAGACGTCAGACGACGACGCCTGGAAGTAG

Alignment

ORF - retro_rnor_390 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFVPAWLNFSTPQSAKSSTATFDKHGEHLSRGEGRFGISRRRHNSSDGFFNNGPLRTTGDSWHQPS
          MAQHDFVPAWLNFSTPQSAKSSTATFDKHGEHLSRGEGRFGISRRRHNSSDGFFNNGPLRTTGDSWHQPS
Retrocopy MAQHDFVPAWLNFSTPQSAKSSTATFDKHGEHLSRGEGRFGISRRRHNSSDGFFNNGPLRTTGDSWHQPS

Parental  LFRHDSVDSGVSKGAYAGTTGNLSGWHGSSRGHDGMSQRAGGSTGNHRHWNGSFHSRKGCAFQEKTPTEI
          LFRHDSVDSGVSKGAYAGTTGNLSGWHGSSRGHDGMSQR.GGSTGNHRHWNGSFHSRKGCAFQEKTPTEI
Retrocopy LFRHDSVDSGVSKGAYAGTTGNLSGWHGSSRGHDGMSQRGGGSTGNHRHWNGSFHSRKGCAFQEKTPTEI

Parental  REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGTPSGVWENPPSAKQPSKMLVIKKISKEDPAAAF
          REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGTPSGVWENPPSAKQPSKMLVIKKISKEDPAA.F
Retrocopy REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGTPSGVWENPPSAKQPSKMLVIKKISKEDPAATF

Parental  SAAFTSGSHHANGNKVSTMVPSVYKNLVPKPAPPPSKPNAWKANRMEHKPGSLSSSREAALTNPVSVTKP
          SAAFTSGSHHANGNKVSTMVPSVYKNLVPKPAPPPSKPNAWKANRMEHKPGSLSSSREAALTNPVSVTKP
Retrocopy SAAFTSGSHHANGNKVSTMVPSVYKNLVPKPAPPPSKPNAWKANRMEHKPGSLSSSREAALTNPVSVTKP

Parental  VVLAAGVVLNAPKESPSSTTPPIEISSSRLTKLTRRTTDRKSEFLKTLKDERNEDCSQSRDCDKLEGLRL
          VVLAAGVVLNAPKESPSSTTPPIEISSSRLTKLTRRTTDRKSEFLKTLKDERNEDCSQSRDCDKLEGLRL
Retrocopy VVLAAGVVLNAPKESPSSTTPPIEISSSRLTKLTRRTTDRKSEFLKTLKDERNEDCSQSRDCDKLEGLRL

Parental  EGSHTPEPKENGEQGCLQNGLSLPMVEEREVLSHSLEAEHRLLKAMGWQEYPENDESCLPLTEDELKEFH
          EGSHTPEPKENGEQGCLQNGLSLPMVEEREVLSHSLEAEHRLLKAMGWQEYPENDESCLPLTEDELKEFH
Retrocopy EGSHTPEPKENGEQGCLQNGLSLPMVEEREVLSHSLEAEHRLLKAMGWQEYPENDESCLPLTEDELKEFH

Parental  TRTEQLRRNGFVKNGFLQGRSSSLFSPWRSTCIAECEDSDTETSSSETSDDDAWK
          TRTEQLRRNGFVKNGFLQGRSSSLFSPWRSTCIAECEDSDTETSSSETSDDDAWK
Retrocopy TRTEQLRRNGFVKNGFLQGRSSSLFSPWRSTCIAECEDSDTETSSSETSDDDAWK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	6.76 RPM
SRP017611_kidney	0.00 RPM	13.19 RPM
SRP017611_liver	0.00 RPM	7.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_390 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390 ,
Sorex araneus	ENSSARG00000004852	1 retrocopy	retro_sara_242,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,
Tursiops truncatus	ENSTTRG00000012202	1 retrocopy	retro_ttru_1355,