RetrogeneDB ID: retro_rnor_2400

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:129511247..129511850(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Serpinb5
• Ensembl ID: ENSRNOG00000002640
• Aliases: Serpinb5, Maspin, PI-5, Pi5
• Description: serpin B5 [Source:RefSeq peptide;Acc:NP_476449]

Sequence

>retro_rnor_2400
TTTCCAGAATCAGAAACAAATGAATGTTCATTCAGAATCAATAAGACAGACAGCAATCCAGTACAAATGATGAATCTTGA
GGCCACCTTCTGCTTGGATAATATTGATGACATCAGCTGCAAGATCATAGAACTTCCTTTCCAGAATAAAATTCTCAGTA
TGCTCACTGTGCTCCCCAAGGACATGGTAGAGCAGTCCATGGGCCTGGAGAACATTGAAAAGGAACTCAATTCAGAAACA
TTGTTATTGTAGACCAACCCCAGCTCTATGGCCAACGCCAAAGTCAAACTCTCCCTTCCAAAGGTTAAGGTAGAAAAGAT
GATTGACCCCAAGGTTAGTCTGGAAAACCTAGGGCTGAGAAGTCTCTTCAATGAAAGTACAGCAGATTTCTCTGGAGTGT
CAGAGACCAAGGGAGTGTCCCTATCAAATGTAATTATCAGAATATACCTATAAATAATTAAAGATGGTGGTGAGTTCATT
GAGGTGCCAGGGTCCTGGATCTTATATCACAAGGATAAATTCAATACTGACTATCTATTTATTTATATCATTAGATAGAA
CAAAACGTGAAACATCATTCTCTTTGGCAAATTCTGTTCTCCT

Alignment

ORF - retro_rnor_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPESETKECPFRINKTDTKPVQMMNLEATFCLGNIDDINCKIIELPFQNKHLSMLIVLPKDVEDESTGLE
          FPESET.EC.FRINKTD..PVQMMNLEATFCL.NIDDI.CKIIELPFQNK.LSML.VLPKD....S.GLE
Retrocopy FPESETNECSFRINKTDSNPVQMMNLEATFCLDNIDDISCKIIELPFQNKILSMLTVLPKDMVEQSMGLE

Parental  KIEKQLNPETLLQWTNPSTMANAKVKLSLPKFKVEKMIDPKASLESLGLKSLFNESTSDFSGMSETKGVS
          .IEK.LN.ETLL..TNPS.MANAKVKLSLPK.KVEKMIDPK.SLE.LGL.SLFNEST.DFSG.SETKGVS
Retrocopy NIEKELNSETLLL*TNPSSMANAKVKLSLPKVKVEKMIDPKVSLENLGLRSLFNESTADFSGVSETKGVS

Parental  VSNVIHRVCLEITEDGGDSIEVPGSRILQHKDEFKADHPFLFIVRHNKTRNIVFLGKFSSP
          .SNVI.R..L.I..DGG..IEVPGS.IL.HKD.F..D..F..I.R.NKT.NI...GKF.SP
Retrocopy LSNVIIRIYL*IIKDGGEFIEVPGSWILYHKDKFNTDYLFIYIIR*NKT*NIILFGKFCSP

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.42 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2400 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2400 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
Cavia porcellus	ENSCPOG00000013882	1 retrocopy	retro_cpor_1174,
Rattus norvegicus	ENSRNOG00000002640	1 retrocopy	retro_rnor_2400 ,
Rattus norvegicus	ENSRNOG00000016581	1 retrocopy	retro_rnor_1895,
Ictidomys tridecemlineatus	ENSSTOG00000007438	1 retrocopy	retro_itri_115,