RetrogeneDB ID: retro_ggor_1747

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:110963809..110965458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA9
• Ensembl ID: ENSGGOG00000014154
• Aliases: None
• Description: None

Sequence

>retro_ggor_1747
GATCCTGAAGTACAGAAAGATATTAAAAATATTCCCTTTAAAATTGTCTGTGCCTCCAATGGTGATGCCTGGGTTGAGGC
TCATGGGAAACTGTATTCTCCAAGTCAGATCGGAGCATTTGTGTCCATGAAGATGAAAGAGACTGCAGACAATTACTTGG
GGCACACAGCAAAAAATGCTGTGATCGCAGTCCCAGCTTATTTCAATGACTTGCAGAGGCAGGCCACTAAAGATGCTGGC
CAGATATCTGGACTGAATGTGCTTCGGGTGATTAGTGAACCCACAGCTGCTGCTCTTGCCTATGGTCTAGACAAATCAAA
AGACAAAGTCATTGCTGTATATGATTTAGGTGGTGGAACTTTTGATATTTCTATCCTGGAATTTCAGAAAGGAGTATTCG
AGGTGAAATCCACAAATGGGGACACTTTCTTAGGTGGGGAAGACTTTGACCAGGCCTTGCTACAGCACATTGTGAAGGAG
TTCAAGAGAGAGATGGGGGTTGATTTGACCAAAGACAACGTGGCATTTCAGAGGGTGCGGGAAGCTGCTGAAAAGGCTAA
ATGTGAACTCTCCTCATCTGTGCAGACTGACATCAATTTGCCCTATCTTACAATGGATTCTTCTGGACCCAAGCATTTGA
ATATGAAGTTGACCCATGCTCAATTTGAAGGGATTGTCACTGATCTAATCAGGAGGACTATCGCTCCATGCCAAAAAGCT
ATGCAAGATGCAGAAGTCAGCAAGAGTGATATAGGAGAAGTGATTCTTGTGGATGGCATGACTAGGATGCCCAAGGTTCA
ACAGACTGTGCAGGACTCTTTTTTGGCAGAGCCCCCAAGTACAGCTGTCAATCCTGAAGAGGCTGTGGCCATTGGAGCTG
CCATTCAGGGAGATGTGTTGGCCGGCGATGTCACAGATGTGCTGCTCCTTGATGTCACTCCCCTGTCTCTGGGTATTGAA
ACTCTGCGAGGTGTCTTTACCAAACTTATTAATAGGAATACCACTATTCCAACCAAGAGCCAGGTATTCTCAACTGCTGC
TGATGGGCAGACACAAGTGGAAATTAAAGTGTGTCAGGGTGAGAGAGAGACGGCTGGAGACAACAAACTCCTTGGACAGT
TTACTTTGATTGGAATTCCACCAGCCCCTCGTGGAGTTCCTCAGATCGAAGTTACATTTGACATTGATGCCAATGGGATC
ATACATGTTTCAGCTAAAGATAAAGGCACAGGACGTGAACAGCAGATTGTAATCCAGTCTTCTGGTGGGTTAAGCAAAGA
TGATGTTGAAAATATGGTTAAAAATGCAGAGAAATATGCTAAGGAAGACCAGCAAAAGAAGGAATGAGTTGAAGCAGTTA
ATATGGCTGAAGGAATCATTCAAGACACAGAAACCAAGATGGAAGAATTCAAGGACCAATTACCTGCTGATAGTGCAACA
AGCTGAAAGAAGAGATTTGCAAAGTAAGGGAGCTCCTAGCTAAAAAAGACAGTGAAACAGGAGAAAACATTAGACAGGCA
GCATCCTCTCATCAGCAGGCATCATTGAAGCTCTTCAAAATGGCATACAAAAAGATGGCATCTGAGCGAGAAGGCTCTGG
AAGTTCTGGCACTGGGGAACAAAAGGAAGATCAAAAGGAGGAAAAACAG

Alignment

ORF - retro_ggor_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 80.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPEVQKDIKNVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLGHTAKNAVITVPAYFND
          DPEVQKDIKN.PFKIV.ASNGDAWVEAHGKLYSPSQIGAFV.MKMKETA.NYLGHTAKNAVI.VPAYFND
Retrocopy DPEVQKDIKNIPFKIVCASNGDAWVEAHGKLYSPSQIGAFVSMKMKETADNYLGHTAKNAVIAVPAYFND

Parental  SQRQATKDAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQKGVFEVKSTNG
          .QRQATKDAGQISGLNVLRVI.EPTAAALAYGLDKS.DKVIAVYDLGGGTFDISILE.QKGVFEVKSTNG
Retrocopy LQRQATKDAGQISGLNVLRVISEPTAAALAYGLDKSKDKVIAVYDLGGGTFDISILEFQKGVFEVKSTNG

Parental  DTFLGGEDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDSSGP
          DTFLGGEDFDQALL.HIVKEFKRE.GVDLTKDN.A.QRVREAAEKAKCELSSSVQTDINLPYLTMDSSGP
Retrocopy DTFLGGEDFDQALLQHIVKEFKREMGVDLTKDNVAFQRVREAAEKAKCELSSSVQTDINLPYLTMDSSGP

Parental  KHLNMKLTRAQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQDLF-GRAPS
          KHLNMKLT.AQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILV.GMTRMPKVQQTVQD.F....PS
Retrocopy KHLNMKLTHAQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVDGMTRMPKVQQTVQDSFLAEPPS

Parental  KAVNPDEAVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADG
          .AVNP.EAVAIGAAIQG.VLAGDVTDVLLLDVTPLSLGIETL.GVFTKLINRNTTIPT.KSQVFSTAADG
Retrocopy TAVNPEEAVAIGAAIQGDVLAGDVTDVLLLDVTPLSLGIETLRGVFTKLINRNTTIPT-KSQVFSTAADG

Parental  QTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQQIVIQ
          QTQVEIKVCQGERE.AGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGI.HVSAKDKGTGREQQIVIQ
Retrocopy QTQVEIKVCQGERETAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIIHVSAKDKGTGREQQIVIQ

Parental  SSGGLSKDDIENMVKNAEKYAEEDRRKKERVEAVNMAEGIIHDTETKMEEFKDQLPADE-CNKLKEEISK
          SSGGLSKDD.ENMVKNAEKYA.ED..KKE.VEAVNMAEGII.DTETKMEEFKDQLPAD..CNKLKEEI.K
Retrocopy SSGGLSKDDVENMVKNAEKYAKEDQQKKE*VEAVNMAEGIIQDTETKMEEFKDQLPADS<CNKLKEEICK

Parental  MRELLARKDSETGENIRQAASSLQQASLKLFEMAYKKMASEREGSGSSGTGEQKEDQKEEKQ
          .RELLA.KDSETGENIRQAASS.QQASLKLF.MAYKKMASEREGSGSSGTGEQKEDQKEEKQ
Retrocopy VRELLAKKDSETGENIRQAASSHQQASLKLFKMAYKKMASEREGSGSSGTGEQKEDQKEEKQ

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	0.10 RPM	214.45 RPM
SRP007412_cerebellum	0.08 RPM	125.37 RPM
SRP007412_heart	0.13 RPM	99.06 RPM
SRP007412_kidney	0.25 RPM	332.59 RPM
SRP007412_liver	0.03 RPM	199.55 RPM
SRP007412_testis	0.62 RPM	246.05 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1747 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2214
Pan troglodytes	retro_ptro_1680

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 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	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747 ,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797,