RetrogeneDB ID: retro_rnor_1895

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:84360554..84361229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Serpinb1a
• Ensembl ID: ENSRNOG00000016581
• Aliases: None
• Description: Leukocyte elastase inhibitor A [Source:UniProtKB/Swiss-Prot;Acc:Q4G075]

Sequence

>retro_rnor_1895
GACAGTATGACCAAACTTGTGCTAGTGAATTCCATCTACTTCAAGGGAATGTGGAAGGAGAAATTTATGGGACAGGACAC
AACAGAATCTCCATTGTGTCTGAATAAGAAAGATTAAAATAACAGTGAAGATGCTGTATCAAAAGAAAATGTTCCATTTC
ATTACATTTTGGACCTGAAGTGCAAGGTGCTGGAGATGCCTTACCAGGGTGGAGAACTTAGTATAATCATCTTGCTGCCC
GAAGACACTAAGGACCAGTCCACGGGTCTTGAGCAGATTGAATAGCAAATAATTTTGGAAAAATTTCATGAATGGGTGAA
ACGTGAGAACTTGGGAAACATTGATGTCCATGCCAAATTGCCCAGGTTCAAGATGGAAGAGATCTACCTTCTCAACTCCA
AACTGGCAGCATGGGAGTGCAGGATCTCTTTAACAGTAGCGGAGCTGGTCTACCTGGATGCCAAGATCCAGAGATCTTTT
CATATCAAAAATTGTCCGCAAGTCCTTTGTGGAAGTGAATGAGGAGGGAACGGAGGTAGCCGCTGTCAAGACTGGCATAG
TTATTGGATACTACCTGAGGACACAGGAAGAATTCATAATGGACCATTCATTCCTTTTCTTTATTCGGCATAACCAAATG
CTAATGTGCTCTTCCTTGGCAGGGTTTATTCCCCA

Alignment

ORF - retro_rnor_1895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DSMTKLVLVNAIYFKGMWEEKFMKQDTTDAPFRLNKKNTKS-VKMMYQKKKFFF-GYISDLKCKVLEMPY
          DSMTKLVLVN.IYFKGMW.EKFM.QDTT..P..LNKK.....VKM.YQKK.F.F..YI.DLKCKVLEMPY
Retrocopy DSMTKLVLVNSIYFKGMWKEKFMGQDTTESPLCLNKKD*NN>VKMLYQKKMFHF<HYILDLKCKVLEMPY

Parental  QGGELSMVILLPEDIEDESTGLKKIEEQITLEKLREWTKRENLENIDVHVKLPRFKIEESYILNSNL-GR
          QGGELS..ILLPED..D.STGL..IE.QI.LEK..EW.KRENL.NIDVH.KLPRFK.EE.Y.LNS.L.G.
Retrocopy QGGELSIIILLPEDTKDQSTGLEQIE*QIILEKFHEWVKRENLGNIDVHAKLPRFKMEEIYLLNSKL<GS

Parental  LGLQDLFNSSKADLSG-MSGSRDLFISKIVHKAFVEVNEEGTEAAAATAGIATFCMLLPEEEFTADHPFI
          .G.QDLFNSS.A.L.G.M..SRDLFISKIV.K.FVEVNEEGTE.AA...GI.....L...EEF..DH.F.
Retrocopy MGVQDLFNSSGAGLPG<MPRSRDLFISKIVRKSFVEVNEEGTEVAAVKTGIVIGYYLRTQEEFIMDHSFL

Parental  FFIRHN-PTANVLFLGRVCSP
          FFIRHN.P.ANVLFLGRV.SP
Retrocopy FFIRHN<PNANVLFLGRVYSP

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	0.65 RPM
SRP017611_kidney	0.00 RPM	19.47 RPM
SRP017611_liver	0.00 RPM	0.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1895 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1895 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000016858	1 retrocopy	retro_mluc_315,
Otolemur garnettii	ENSOGAG00000009416	1 retrocopy	retro_ogar_323,
Rattus norvegicus	ENSRNOG00000002640	1 retrocopy	retro_rnor_2400,
Rattus norvegicus	ENSRNOG00000016581	1 retrocopy	retro_rnor_1895 ,