RetrogeneDB ID: retro_ptro_1680

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:227046525..227048172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA9
• Ensembl ID: ENSPTRG00000017290
• Aliases: HSPA9, HSPA9B
• Description: None

Sequence

>retro_ptro_1680
GATCCTGAAGTACAGAAAGACATTAAAAATATTCCCTTTAAAATTGTCTGTGCCTCCAATGGTGATGCCTGGGTTGAGGC
TCATGGGAAACTGTATTCTCCAAGTCAGATCGGAGCATTTGTGTCGATGAAGATGAAAGAGACTGCAGAAAATTACTTGG
GCCCACAGCAAAAAATGCTGTGATCGCAGTCCCAGCTATTTCAATGACTTGCAGAGGCAGGCCACTAAAGATGCTGGCCA
GATATCTGGACTGAATGTGCTTCAGGTGATTAATGAACCCACAGCTGCTGCTCTTGCCTATGGTCTAGACAAATCAAAAG
ACAAAGTCATTGCTGTATATGATTTAGGTGGTGGAACTTTTGATATTTCTACCCTGGAATTTCAGAAAGGAGTATTCGAG
GTGAAATCCACAAATGGGGACACTTTCTTAGGTGGGGAAGACTTTGACCAGGCCTTGCTACAGCACATTGTGAAGGAGTT
CAAGAGAGAGATGGGGGTTGATTTGACCAAAGACAACGTGGCATTTCAGAGGGTGCGGGAAGCTGCTGAAAAGGCTAAAT
GTGAACTCTCCTCATCTGTGCAGACTGACATCAATTTGCCCTATCTTACAACGGATTCTTCTGGACCCAAGCATTTGAAT
ATGAAGTTGACCCATGCTCAATTTGAAGGGATTGTCACTGATCTAATCAGGAGGACTATCGCTCCATGCCAAAAAGCTAT
GCAAGATGCAGAAGTCAGCAAGAGTGATATAGGAGAAGTGATTCTTGTGGGTGGCATGACTAGGATGCCCAAGGTTCAAC
AGACTGTGCAGGACTTTTTTTGGCAGAGCCCCCAAGTAAAGCTGTCAATCCTGATGAGGCTGCGGCCATTGGAGCTGCCA
TTCAGGGAGATGTGTTGGCTGGCAATGTCACAGATGTGCTGCTCCTTGATGTCACTCCCCTGTCTCTGGGTATTGAAACT
CTGCGAGGTGTCTTTACCAAACTTATTAATAGGAATACCACTATTCCAACCAAGAAGAGCCAGGTATTCTCAACTGCTGC
TGATGGGCAGACACAAGTGGAAATTAAAGTGTGTCAGGGTGAGAGAGAGATGGCTGGAGACAACAAACTCCTTGGACAGT
TTACTTTGATTGGAATTCCACCAGCCCCTCGTGGAGTTCCTCAGATCGAAGTTATATTTGACATTGATGCCAATGGGATC
ATACATGTTTCAGCTAAAGATAAAAGCACAGGACGTGAGCAGCAGATTGTAATCCAGTCTTCTGGTGGGTTAAGCAAAGA
TGATGTTGAAAATATGGTTAAAAATGCAGAGAAATATGCTAAGGAAGACCAGCAAAAGAAGGAACGAGTTGAAGCAGTTA
ATATGGCTGAAGGAATCATTCATGACACAGAAACCAAGATGAAGAATTCAAGGACCAATTACCTTCTGATAGTGCAACAA
GCTGAAAGAAGAGATTTCCAAAGTGAGGGAGCTCCTAGCTAAAAAGACAGTGAAACAGGAGAAAACATTAGACAGGCAGC
ATCCTCTCTTCAGCAGGCATCACTGAAGCTCTTCAAAATGGCATACAAAAAGATGGCATCTGAGCAAGAAGGCTCTGAAA
GTTCTGGCACTGGGGAACAAAAGGAAGATCAAAAGGAGGAAAAACAG

Alignment

ORF - retro_ptro_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.46 %
• Parental protein coverage: 81. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DPEVQKDIKNVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLGH-TAKNAVITVPA-YF
          DPEVQKDIKN.PFKIV.ASNGDAWVEAHGKLYSPSQIGAFV.MKMKETAENYLG..TAKNAVI.VPA.YF
Retrocopy DPEVQKDIKNIPFKIVCASNGDAWVEAHGKLYSPSQIGAFVSMKMKETAENYLGP<TAKNAVIAVPA<YF

Parental  NDSQRQATKDAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQKGVFEVKST
          ND.QRQATKDAGQISGLNVL.VINEPTAAALAYGLDKS.DKVIAVYDLGGGTFDIS.LE.QKGVFEVKST
Retrocopy NDLQRQATKDAGQISGLNVLQVINEPTAAALAYGLDKSKDKVIAVYDLGGGTFDISTLEFQKGVFEVKST

Parental  NGDTFLGGEDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDSS
          NGDTFLGGEDFDQALL.HIVKEFKRE.GVDLTKDN.A.QRVREAAEKAKCELSSSVQTDINLPYLT.DSS
Retrocopy NGDTFLGGEDFDQALLQHIVKEFKREMGVDLTKDNVAFQRVREAAEKAKCELSSSVQTDINLPYLTTDSS

Parental  GPKHLNMKLTRAQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQD-LFGRA
          GPKHLNMKLT.AQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQD..FGRA
Retrocopy GPKHLNMKLTHAQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQD>FFGRA

Parental  -PSKAVNPDEAVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTA
          .PSKAVNPDEA.AIGAAIQG.VLAG.VTDVLLLDVTPLSLGIETL.GVFTKLINRNTTIPTKKSQVFSTA
Retrocopy >PSKAVNPDEAAAIGAAIQGDVLAGNVTDVLLLDVTPLSLGIETLRGVFTKLINRNTTIPTKKSQVFSTA

Parental  ADGQTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQQI
          ADGQTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEV.FDIDANGI.HVSAKDK.TGREQQI
Retrocopy ADGQTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVIFDIDANGIIHVSAKDKSTGREQQI

Parental  VIQSSGGLSKDDIENMVKNAEKYAEEDRRKKERVEAVNMAEGIIHDTETKM-EEFKDQLPADE-CNKLKE
          VIQSSGGLSKDD.ENMVKNAEKYA.ED..KKERVEAVNMAEGIIHDTETKM.EEFKDQLP.D..CNKLKE
Retrocopy VIQSSGGLSKDDVENMVKNAEKYAKEDQQKKERVEAVNMAEGIIHDTETKM<EEFKDQLPSDS<CNKLKE

Parental  EISKMRELLAR-KDSETGENIRQAASSLQQASLKLFEMAYKKMASEREGSGSSGTGEQKEDQKEEKQ
          EISK.RELLA..KDSETGENIRQAASSLQQASLKLF.MAYKKMASE.EGS.SSGTGEQKEDQKEEKQ
Retrocopy EISKVRELLAK<KDSETGENIRQAASSLQQASLKLFKMAYKKMASEQEGSESSGTGEQKEDQKEEKQ

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	122.10 RPM
SRP007412_cerebellum	0.14 RPM	166.70 RPM
SRP007412_heart	0.09 RPM	254.13 RPM
SRP007412_kidney	0.08 RPM	257.33 RPM
SRP007412_liver	0.10 RPM	306.23 RPM
SRP007412_testis	0.53 RPM	94.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1680 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1680 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2214
Gorilla gorilla	retro_ggor_1747

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 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	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680 ,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797,