RetrogeneDB ID: retro_rnor_83

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:54966072..54967389(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004092
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Mfap1a
• Ensembl ID: ENSRNOG00000015984
• Aliases: Mfap1a, RGD1562232
• Description: microfibrillar-associated protein 1 [Source:RefSeq peptide;Acc:NP_001178893]

Sequence

>retro_rnor_83
ATGTCGGTCCCAAGCACACTCATGAAGCAGCCGCCCATTCAGTCTACGGCTGGGGCAGTCCCAGTACGCAATGAGAAAGG
TGAGATTTCAATGGAAAAAGTGAAGGTAAAACGTTATGTGTCCGGAAAAAGACCAGATTATGCCCCTATGGAGTCCTCAG
ATGAAGAGGATGAAGAATTTCAGTTCATTAAGAAAGCTAAGGAACAAGAAGCAGAGCCTGAGGAACAGGAGGAGGACTCA
TCTAGTGATCCCCGACTTCGGCGTTTACAGAACCGCATTAGTGAAGATGTGGAAGAGAGATTGGCTCGACACAGAAAAAT
AGTGGAACCTGAAGTAGTAGGTGAAAGTGACTCAGAAGTAGGAGATGCTTGGCGTATGGAACGAGAAGATAGTAGTGAGG
AAGAAGAGGAAGAAATTGACGATGAAGAAATAGAGCGGCGCCGTGGCATGATGCGGCAGCGAGCACAGGAGAGGAAAAAT
GAAGAGATGGAAGTCATGGAGGTGGAAGATGAAGGACGTTCTGGGGAGGAGTCAGAGTCAGAGTCTGAGTATGAGGAGTA
CACAGACAGTGAAGATGAAATGGAGCCTCGACTTAAGCCTGTCTTCATTCGAAAGAAGGATCGGGTGACAGTTCAAGAAC
GAGAAGCTGAAGCATTGAAGCAGAAGGAACTGGAACAGGAAGCAAAACGCATGGCTGAGGAGCGGCGCAAGTACACCCTC
AAGATTGTAGAAGAAGAGACCAAGAAAGAGCTAGAGGAGAACAAGCGGTCCCTTGCCGCCCTGGATGCACTCAATACTGA
TGATGAAAATGACGAGGAGGAGTATGAAGCGTGGAAGGTCCGCGAGCTCAAAAGAATCAAGCGAGACAGAGAAGACCGAG
AAGCGCTTGAAAAGGAGAAAGCAGAAATTGAACGCATGAGAAACCTGACTGAGGAAGAAAGGCGGGCTGAACTTCGGGCA
AATGGCAAAGTCATTACCAACAAAGCTGTGAAAGGCAAATACAAGTTTTTACAAAAGTATTATCATCGAGGTGCCTTCTT
CATGGATGAGGATGAAGAAGTTTACAAGAGAGATTTTAGCGCACCCACTCTTGAGGACCATTTCAACAAAACTATTCTTC
CAAAAGTCATGCAGGTCAAGAATTTTGGACGGTCCGGTCGCACCAAGTACACCCACCTTGTGGATCAAGATACCACTTCC
TTTGACTCTGCATGGGGCCAAGAGAGTGCACAGAACACAAAATTCTTTAAACAAAAGGCAGCAGGGGTACGAGATGTATT
TGAACGACCATCTGCTAAGAAGAGGAAAACCACCTAG

Alignment

ORF - retro_rnor_83 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVPSALMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKEQE
          MSVPS.LMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKEQE
Retrocopy MSVPSTLMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKEQE

Parental  AEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEVEGDAWRLEREDSSEEEEEEI
          AEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEV.GDAWR.EREDSSEEEEEEI
Retrocopy AEPEEQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVEPEVVGESDSEV-GDAWRMEREDSSEEEEEEI

Parental  DDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRV
          DDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRV
Retrocopy DDEEIERRRGMMRQRAQERKNEEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRV

Parental  TVQEREAEALRQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWK
          TVQEREAEAL.QKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWK
Retrocopy TVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWK

Parental  VRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFMD
          VRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFMD
Retrocopy VRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFMD

Parental  EDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK
          EDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK
Retrocopy EDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQK

Parental  AAGVRDVFERPSAKKRKTT
          AAGVRDVFERPSAKKRKTT
Retrocopy AAGVRDVFERPSAKKRKTT

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	30.20 RPM
SRP017611_kidney	0.07 RPM	22.26 RPM
SRP017611_liver	0.00 RPM	11.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_83 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_83 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_83 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83 ,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001, retro_tbel_3246,