RetrogeneDB ID: retro_rnor_1797

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:80930678..80932106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hspa9
• Ensembl ID: ENSRNOG00000019525
• Aliases: Hspa9, Hspa9a
• Description: stress-70 protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001094128]

Sequence

>retro_rnor_1797
TCACAGTGACAGGCCACTAAGGATGCTGGCCAGATATCTGGGCTAAACATGCTCCGAGTGATCAACGAGCCTACAGCTGC
TGCTCTGGCTCACGGTCTGGACAAATCCGAAGATAAAGTCATTGNNNNNNNNNNNNNNANNNNNNNNNNNNNNANNNNNN
NNNNNCTAGAAATTCAGAAAGGAGTGTTTGAGGTGAAATCCACCAATGGGGACACTTTCTTAGGAGGTGAAGACTTTAAC
CAAGGTTTATTACGGCACATTGTCAAGGAGTTCAAGAGGGAGACAGGGGTTGATTTGATCAAAGACAGCATGGCACTTCA
GAGAGTTCGGGAAGCTGCTGAGAAGGCTAAATGTGAGCTCTCCTCATCTGTACAGACTGACATCAACTTGCCATACGTTA
CAATGGATGCAATGGATGCTTCTGGACCAAAGCATTTGAATATGAAGTTGACTCGAGCTCAGTTTGAAGGCATTGTCACA
GATCTAATCAAGAGAATTATTGCTCCGTGTCAGAAAGCTATGCAGGATGCAGAAGTCAGCAAGAGTGACATAGGAGAAGT
GATTCTGATGGTGGCATGACGAGGATGCCCAGGTTCAGCAGACTGTGCAAGATCTTTGTGGCAGAGCCCTGAGTAAAGCT
GTTAATCCTGATGAGGCTGTAGCCATTGGAACTGCCATTCAAGGGGGTGTGTTGGCTGGTGATGTTACAGATGTGCTACT
CTTGGATGTCACTCCCCTCTCTCTAGGTATTGAGACACTGGGAGGTGTTTTTACCAAGCTTATTAATAGGAACACCACTT
TTCCAACCAAAAAGAGCCAGGTGTTTTCTACTGCTGCTGATGGACAAACTCAAGTAGAGATTAAAGTGTGTCAGGGGAAA
GAGAGATGGCCGGAGACAACAAACTTTTAGGCCAGTTCACTTTGATTGGAATTCCCCCAGCCCCTCGTGGAGTGCCTCAG
ATTGAAGTTCCATTTGACATTGATGCAAATGGGATTGTGCACATTTCTGCCAAAGATAAAGGGACAGGACGAGAGCAACA
GATTGTAATCCAGTCTTCTGATGGATTAAGCAAAGATGATATTGAAAATATGGTTTAAAATGCAGAGAAGTATGCTGAAG
AAGACCAGAGAAAGAAGGAACGTGTTGAAGCAGTTAATATGGCTGAAGGAATTATTCATGACACAGAAACGAAGCCTGCT
GACGAGTGCAACAAGCTAAAGGAAGAGACTTCCAAAATGAGAGAACTCCTTGCTCGAAAGGACAGTGAAACAGGAGAAAA
CATTAGGCAGGCGGCATCTTCCCTTCAGAAGGCATCATTGAAACTCTTAGAAATGGCATATTAAAAGATGGCATCTGAAC
GGGAAGGTTCTGGAAGTTCTAGCACTGGGGAACAGAAGGAAGATCAGAAGGAAGAAAAACAGTAAGAG

Alignment

ORF - retro_rnor_1797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 70.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQRQATKDAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQKGVFEVKSTNG
          SQ.QATKDAGQISGLN.LRVINEPTAAALA.GLDKSEDKVI..............LEIQKGVFEVKSTNG
Retrocopy SQ*QATKDAGQISGLNMLRVINEPTAAALAHGLDKSEDKVIXXXXXXXXXXXXXXLEIQKGVFEVKSTNG

Parental  DTFLGGEDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDA---
          DTFLGGEDF.Q.LLRHIVKEFKRETGVDL.KD.MALQRVREAAEKAKCELSSSVQTDINLPY.TMDA...
Retrocopy DTFLGGEDFNQGLLRHIVKEFKRETGVDLIKDSMALQRVREAAEKAKCELSSSVQTDINLPYVTMDAMDA

Parental  SGPKHLNMKLTRAQFEGIVTDLIKRTIAPCQKAMQDAEVSKSDIGEVILV-GGMTRMPK-VQQTVQDLFG
          SGPKHLNMKLTRAQFEGIVTDLIKR.IAPCQKAMQDAEVSKSDIGEVIL..GGMTRMP..VQQTVQDL.G
Retrocopy SGPKHLNMKLTRAQFEGIVTDLIKRIIAPCQKAMQDAEVSKSDIGEVILM<GGMTRMPR<VQQTVQDLCG

Parental  RAPSKAVNPDEAVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFST
          RA.SKAVNPDEAVAIG.AIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTT.PTKKSQVFST
Retrocopy RALSKAVNPDEAVAIGTAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTFPTKKSQVFST

Parental  AADGQTQVEIKVCQ-GEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQ
          AADGQTQVEIKVCQ.GEREMAGDNKLLGQFTLIGIPPAPRGVPQIEV.FDIDANGIVH.SAKDKGTGREQ
Retrocopy AADGQTQVEIKVCQ<GEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVPFDIDANGIVHISAKDKGTGREQ

Parental  QIVIQSSGGLSKDDIENMVKNAEKYAEEDRRKKERVEAVNMAEGIIHDTETKMEEFKDQLPADECNKLKE
          QIVIQSS.GLSKDDIENMV.NAEKYAEED.RKKERVEAVNMAEGIIHDTETK.......L...E..K..E
Retrocopy QIVIQSSDGLSKDDIENMV*NAEKYAEEDQRKKERVEAVNMAEGIIHDTETKPADECNKL-KEETSKMRE

Parental  EISKMRELLARKDSETGENIRQAASSLQQASLKLFEMAYKKMASEREGSGSSSTGEQKEDQKE
          ......................A..SL.........MA.....S.....G........E.Q.E
Retrocopy LLARKDSETGENIRQAASSLQKA--SLKLLEMAY*KMASEREGSGSSSTGEQKEDQKEEKQ*E

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	0.07 RPM	114.10 RPM
SRP017611_kidney	0.56 RPM	398.46 RPM
SRP017611_liver	0.20 RPM	233.78 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1797 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1797 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1797 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013579	2 retrocopies	retro_chof_2539, retro_chof_293,
Homo sapiens	ENSG00000113013	1 retrocopy	retro_hsap_2214,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797 ,