RetrogeneDB ID: retro_rnor_1012

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:78265476..78266027(+)
• Located in intron of: ENSRNOG00000004781

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Glo1
• Ensembl ID: ENSRNOG00000000541
• Aliases: None
• Description: Lactoylglutathione lyase [Source:UniProtKB/Swiss-Prot;Acc:Q6P7Q4]

Sequence

>retro_rnor_1012
ATGGCAGAGCCACAGCCAGCGTCCAGTGGCCTCACTGATGAGGCCGCCCTCAACTGCTGCTCTGCCCCAGACCCAAGCAC
CAAGGATTTGCTACTGCAGCAAACGATGCTAAGAATTAAGGATCCTAAGAAGCCCCTGGATTTTTATATGAAGGTTCTTG
GACTGATGCTTCTCCAGCAGCTTGACTTTCCTTCTATGAAGTTCTCGCTCTATTTCTTAGCATACGAGGATAAGAATGAT
AGTCTCAAGGACAAGATGGAGAGGACAGCATGGACTTCTACCAGAAAGACTACCCTGGAGCTCACACACAACTGAGGCAC
TGAAGATGATGAGACCCAGAGTTATCACAACAGCAACTTGGACCCTCGGGGATTGGTCACATTGGCATTGCCGTTCCTGA
TGTCTATGGAGCCTGTAAGAGATTTGAAGAACTAGGTGTCAAGTTTGTGAAGAAGCCTGATGATGGGAAAATGAAAGGAC
TGGAATTCATTCAAGATCCTGACGGCTCCTGGATTGAAATTCTGAATCCTAACGAAATAGCATTAATTATT

Alignment

ORF - retro_rnor_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEPQPASSGLTDEAALSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPSMKFSL
          MAEPQPASSGLTDEAAL.CCS.PDPSTKD.LLQQTMLRIKDPKK.LDFY..VLGL.LLQ.LDFPSMKFSL
Retrocopy MAEPQPASSGLTDEAALNCCSAPDPSTKDLLLQQTMLRIKDPKKPLDFYMKVLGLMLLQQLDFPSMKFSL

Parental  YFLAYEDKNDIPKDKTERTAWAFSRKATLELTHNWGTEDDETQSYHNGNSDPR-GFGHIGIAVPDVYEAC
          YFLAYEDKND..KDK.ERTAW...RK.TLELTHN.GTEDDETQSYHN.N.DPR.G.GHIGIAVPDVY.AC
Retrocopy YFLAYEDKNDSLKDKMERTAWTSTRKTTLELTHN*GTEDDETQSYHNSNLDPR<GIGHIGIAVPDVYGAC

Parental  KRFEELGVKFVKKPDDGKMKGLAFVQDPDGYWIEILNPNKMATII
          KRFEELGVKFVKKPDDGKMKGL.F.QDPDG.WIEILNPN..A.II
Retrocopy KRFEELGVKFVKKPDDGKMKGLEFIQDPDGSWIEILNPNEIALII

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	67.80 RPM
SRP017611_kidney	0.00 RPM	58.83 RPM
SRP017611_liver	0.00 RPM	47.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1012 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012 , retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,