RetrogeneDB ID: retro_ggor_2643

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:4631631..4632889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSGGOG00000024392
• Aliases: None
• Description: None

Sequence

>retro_ggor_2643
ATACTGAACACTGGTAAAAAATTGTATGAGGGTAAAACAAAAGAAGTCTACGAATTGTTAGATAGTCCAGGAAAAGTCCT
CCTGCAGTCCAAGGACAAGATTACAGCAGGAAATGTAGCTAGAAAGAATCACCTGGAAGGAAAAGCTGCAATCTCAAATA
AAATCACCAGTTGTATTTTTCAGTTATTATAGGAAGCAGGTATTAAAACTTCCTTCACCAGAAAATGTGGGGAGACAGCT
TTCATTGCACCCCACTGTGAAATGATTCCAATTCAATGGGTTTGCAGAAGAATAGCAACTGGTTCTTTTCTCAAAAGAAA
TCCTGGTGTCAAGGAAGGATATAAGTTTACCCACTTAAAGTGGAGTTGTTTTTCAAGGATGATGCCAATAATGACCCACA
GTGGTCTGAGGAACAGCTGATTGCTGCAAAATTTTGCTTTGCTGGACTTGTTATAGGCCAGACTGAAGTGGATATCAGGA
GTCATGCTACACAGGCTATATTTGAAATACTGGAGAAATCCTGGTTGCCCCAGAATTGTACACTGGTTGATATGAAGATT
GAATTTGGTGTTGATGTAACCACAAAGAAATTGTTCTTGCTGATGTTATTGACAATGATTCCTGGAGACTGTGGCCATCA
GGAGATCGAAGCCAACAGAAAGACAAACAGTCTTATCAGGACCTCAAAGAAGTAACTCCTGAAGGGCTCCAAATGGTAAA
GAAAAACTTTGAGTGGGTTGCAGAGAGAGTAGAGTTGCTTTTGAAATCAGAAAGTCAGTGCAGGGTTGTAGTGTTGATGG
GCTCTACTTCTGATCTTGGTCACTGTGAAAAAATCAAGAAGGCCTGTGGAAATTTTGGCATTCCATGTGAACTTTGAGTA
ACATTTGTGCATAAAGGACCAGATGAAACTCTGCGGATTAAAGCTGAGTACGAAGGGGATGGCATTCCTACTGTATTTGT
GGCAGTGGCAGGCAGAAGTAATAGTTTGGGACCAGTGATGTATGGAAACACTGCATATCCAGGTAGCGGCTGTCCTCCCC
TCACACCAGACTGGGGAGCTCAGGATGTGTGGTCTTCTCTTCGACTACCCAGTGGTCTTGGCTGTTCAACCATACTTTCT
CAAGAAGGATCAGCTCAATTTGCTGCTCAGATATTTGGGTTAAACGATCATTTAGTATGGAGCAAACTGTGAGCAAGCAT
TTTGAACACATGGATTTCCTTGAAGCAGGCTGACAAGAAAATCAGAGAATGTAATTTA

Alignment

ORF - retro_ggor_2643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLNIGKKLYEGKTKEVYELLDSPGKVLLQSKDQITAGNAARKNHLEGKAAISNKITSCIFQLLQEAGIKT
          .LN.GKKLYEGKTKEVYELLDSPGKVLLQSKD.ITAGN.ARKNHLEGKAAISNKITSCIFQLL.EAGIKT
Retrocopy ILNTGKKLYEGKTKEVYELLDSPGKVLLQSKDKITAGNVARKNHLEGKAAISNKITSCIFQLL*EAGIKT

Parental  AFTRKCGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYKF-YPPKVELFFKDDANNDPQWSEEQ
          .FTRKCGETAFIAP.CEMIPI.WVCRRIATGSFLKRNPGVKEGYKF.YP.KVELFFKDDANNDPQWSEEQ
Retrocopy SFTRKCGETAFIAPHCEMIPIQWVCRRIATGSFLKRNPGVKEGYKF<YPLKVELFFKDDANNDPQWSEEQ

Parental  LIAAKFCFAGLVIGQTEVDIMSHATQAVFEILEKSWLPQNCTLVDMKIEFGVDVTT-KEIVLADVIDNDS
          LIAAKFCFAGLVIGQTEVDI.SHATQA.FEILEKSWLPQNCTLVDMKIEFGVDVTT.KEIVLADVIDNDS
Retrocopy LIAAKFCFAGLVIGQTEVDIRSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTT<KEIVLADVIDNDS

Parental  WRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVKKNFEWVAERVELLLKSE----IVVLMSSTSDLGHCEN
          WRLWPSGDRSQQKDKQSY.DLKEVTPEGLQMVKKNFEWVAERVELLLKSE.....VVLM.STSDLGHCE.
Retrocopy WRLWPSGDRSQQKDKQSYQDLKEVTPEGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDLGHCEK

Parental  I-KACRNVGTPCEL---STHRGPNETLKIKAACEGDGIPTVFVAVAGRSNGLGPVMSGNTAYPVISCPPL
          I.KAC.N.G.PCEL.....H.GP.ETL.IKA..EGDGIPTVFVAVAGRSN.LGPVM.GNTAYP...CPPL
Retrocopy IKKACGNFGIPCEL*VTFVHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNSLGPVMYGNTAYPGSGCPPL

Parental  TPDWGAQDVWSSLRLPSEPIGLGCSTILSPEGSAQFAAQIFGLSNHLVWSKLRASILNTWISLKQADKKI
          TPDWGAQDVWSSLRLPS...GLGCSTILS.EGSAQFAAQIFGL..HLVWSKL.ASILNTWISLKQADKKI
Retrocopy TPDWGAQDVWSSLRLPS---GLGCSTILSQEGSAQFAAQIFGLNDHLVWSKL*ASILNTWISLKQADKKI

Parental  RECNL
          RECNL
Retrocopy RECNL

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	5.04 RPM	10.12 RPM
SRP007412_cerebellum	4.89 RPM	11.15 RPM
SRP007412_heart	0.97 RPM	1.19 RPM
SRP007412_kidney	4.33 RPM	14.11 RPM
SRP007412_liver	4.35 RPM	13.64 RPM
SRP007412_testis	7.15 RPM	26.21 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_2643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2643 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3927
Pan troglodytes	retro_ptro_2670

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643 ,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,