RetrogeneDB ID: retro_ggor_1199

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:37102365..37103293(-)
• Located in intron of: ENSGGOG00000007661

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSGGOG00000028153
• Aliases: None
• Description: None

Sequence

>retro_ggor_1199
ATGAGTTCCACGCAGTTCAACAAGGGCCTCTAGTATGGGCTGTCAGCCGAGGTCAAGAACTGGCTCCTGCCCAAATATGA
CCCCCAGAAGGAGGCAGAGCTCTGCAGCTGGATCAAGGGACTCACCGGCATCTCCATTGACCCTAACTTCCAGAAGAGCC
TGAAGGATGGGATTATCTTATGCATACTCATGAACAAGCTGCAGCCGGCCTCAGTCCCCAAGATCAACCACTCCATGCAG
AAGTGGCACCAGCTGGAAAACCTCTCCAACTTCATCAAGGCTATAGTCAGCTATGACATGAACCCCATGGACCTGTTCGA
GGCCAACAACCTGTTTGAGAGTGGGAACATGAGGCACATGCAGGTGTCTCTTTTTGCCCTAGCAGGGAAGGTCAAGACTA
AGAAGCCGCAGAGCGGGGTGGACATTGGCATCAAGTACTCAGAGAAGCAGGAGCAGAACTTCAGTGACGCCGCCATGAAG
GCCGGCTAGTGCGTCATCGGGCTGCAAATGGGCACCAACAAATGTGCCAGCCAGTTGGGCATGACCGTGTATGGCGTGAG
GAGGCATCTCTGTGACCCCAAGAATCACATCCTGCCCCGCCATGGACCACTCGACCATTAGCCTCCAGATGGGTACAAAT
AAGTGTGCCAGCCAGGTGAGCATGACAGCTCCTGGGACGCAGCAGCACATCTATGACACCAAGCTGGGAACTGACAAGTG
CGAAAATTCCTCCATGTCCCTGCAGATGGGCTACACCCAGGGTACCAACCATAGTAGCCAGGTCTTTGGCCTGGGCCAGC
ATATATGTGACCCCAAGTACTGCCTGCCAGGCACAGTGGCCGATGGGGCTCCCTTGGGTGCTGGCAACTGCCTGGGCCCA
GGAGAGGTCCCTGAATATCCCCCTTACTACCAGGAGGAGGCTGGCTAC

Alignment

ORF - retro_ggor_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPG
          MSSTQFNKG..YGLSAEVKN.LL.KYDPQKEAEL..WI.GLTG.SI.P.FQK.LKDG.ILC.LMNKLQP.
Retrocopy MSSTQFNKGL*YGLSAEVKNWLLPKYDPQKEAELCSWIKGLTGISIDPNFQKSLKDGIILCILMNKLQPA

Parental  SIPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSGV
          S.PKIN.SMQ.WHQLENLSNFIKA.VSY.MNP.DLFEAN.LFESGNM...QVSL.ALAGK.KTK..QSGV
Retrocopy SVPKINHSMQKWHQLENLSNFIKAIVSYDMNPMDLFEANNLFESGNMRHMQVSLFALAGKVKTKKPQSGV

Parental  DIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHIL-PPMDHSTISLQ
          DIG.KYSEKQE.NF.DA.MKAG.CVIGLQMGTNKCASQ.GMT.YG.RRHL.DPKNHIL.P.MDHSTISLQ
Retrocopy DIGIKYSEKQEQNFSDAAMKAG*CVIGLQMGTNKCASQLGMTVYGVRRHLCDPKNHIL>PAMDHSTISLQ

Parental  MGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGTV
          MGTNKCASQV.MTAPGT..HIYDTKLGTDKC.NSSMSLQMGYTQG.N.S.QVFGLG..I.DPKYC..GTV
Retrocopy MGTNKCASQVSMTAPGTQQHIYDTKLGTDKCENSSMSLQMGYTQGTNHSSQVFGLGQHICDPKYCLPGTV

Parental  ADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
          ADGAP.G.G.C..PGEVPEYPPYYQEEAGY
Retrocopy ADGAPLGAGNCLGPGEVPEYPPYYQEEAGY

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	0.00 RPM	7.82 RPM
SRP007412_cerebellum	0.00 RPM	5.12 RPM
SRP007412_heart	0.00 RPM	32.30 RPM
SRP007412_kidney	0.04 RPM	44.49 RPM
SRP007412_liver	0.00 RPM	54.07 RPM
SRP007412_testis	0.00 RPM	10.26 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_1199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1199 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1575
Pan troglodytes	retro_ptro_1061
Pongo abelii	retro_pabe_1299

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612,
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581,
Homo sapiens	ENSG00000064666	16 retrocopies	retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199 , retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Myotis lucifugus	ENSMLUG00000013160	4 retrocopies	retro_mluc_1536, retro_mluc_1965, retro_mluc_2047, retro_mluc_2210,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326,