RetrogeneDB ID: retro_ggor_1612

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 22:14151201..14152119(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000011225
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ggor_1612
ATGAGCTCCACGCAGTTCAACAAGGGACCCTCATATGGCCTGTCGGCTGAGGTCAAGAACCAGCTTCTGTCCAAATATGA
CCCCCAGAAGGAGGCAGAGCTCCACAGCTGGATCAAGGGACTCACAGGCCTCTTCATCGGCCCCGACTTCCAGAAGGGCC
TGAAGGACGGGATTATCTTATGCACACTCATGAACAAGCTACAGCCAGGCTCAGTCCCCAAGATCAATCACTACATGCAG
AACTGGCACCAGCTAGAAAACCTCTTCAACTTCATCAAGGCCATGGTCAGCTACGGATGAACCCCATGGACCTGTTCGAG
GCCAACGACCTGTTTGAGAGTAGAAGTATGACACAGCTGCAGGTGTCTCTTCTCGCCCTGGTGAGGAAGGCCAAGACTAA
GGAGCTGCAGAGCGGGGTGGACACTGGCATCAAGTACTTGGAGAAGCAGGAGTGGAACTCTGACAACCCCCCCTGAAGGC
TGGCCAGTGCATGCTCGGGCTGCAGATGGGCACCAACAAATGTGCCAGCCAGTCAGGGATGACCGCATACAGCATGAGGA
GGCATTTCTACGACCCCAACAACTACATCCTGCCCCCCATGGACCACTCCATCATCAGTGTCCAGATGGGTATAAACAAG
TGTGTCAGCCAGGTGGCCATGACGGCTCCTGGGATGCAGCGGCACATCTCTGACACCAAGCTGGGAACCGACAAGTGTGG
TAACTCCTCCATATCCCTGCAGATGGGTTACACACAGGGCACCAACCAGAGTAGCCAGGTCTTGGCCTGGGCCAGCAGAT
ATACGACCCCAAGTACTGCCCGCAAGGCACAGTGGGGGCTCCCTCAGGCGCTGGCGACTGCCTGGGCCCCGGGGAGGTCC
CTGAATATCCCCCTTACTACCAGGAGGAAGCTGACTAC

Alignment

ORF - retro_ggor_1612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPG
          MSSTQFNKGPSYGLSAEVKN.LLSKYDPQKEAEL..WI.GLTGL.IGPDFQKGLKDG.ILCTLMNKLQPG
Retrocopy MSSTQFNKGPSYGLSAEVKNQLLSKYDPQKEAELHSWIKGLTGLFIGPDFQKGLKDGIILCTLMNKLQPG

Parental  SIPKINRSMQNWHQLENLSNFIKAMVSYG-MNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSG
          S.PKIN..MQNWHQLENL.NFIKAMVSYG.MNP.DLFEANDLFES..MTQ.QVSLLAL..KAKTK.LQSG
Retrocopy SVPKINHYMQNWHQLENLFNFIKAMVSYG<MNPMDLFEANDLFESRSMTQLQVSLLALVRKAKTKELQSG

Parental  VDIGVKYSEKQERNFDD-ATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISL
          VD.G.KY.EKQE.N.D.....KAGQC..GLQMGTNKCASQSGMTAY..RRH.YDP.N.ILPPMDHS.IS.
Retrocopy VDTGIKYLEKQEWNSDN<PPLKAGQCMLGLQMGTNKCASQSGMTAYSMRRHFYDPNNYILPPMDHSIISV

Parental  QMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQV-FGLGRQIYDPKYCPQG
          QMG.NKC.SQV.MTAPG..RHI.DTKLGTDKC.NSS.SLQMGYTQG.NQS.QV..GLG.QIYDPKYCPQG
Retrocopy QMGINKCVSQVAMTAPGMQRHISDTKLGTDKCGNSSISLQMGYTQGTNQSSQV<LGLGQQIYDPKYCPQG

Parental  TVADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
          TV..GAPSG.GDC..PGEVPEYPPYYQEEA.Y
Retrocopy TV--GAPSGAGDCLGPGEVPEYPPYYQEEADY

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	7.82 RPM
SRP007412_cerebellum	0.12 RPM	5.12 RPM
SRP007412_heart	0.03 RPM	32.30 RPM
SRP007412_kidney	0.00 RPM	44.49 RPM
SRP007412_liver	0.45 RPM	54.07 RPM
SRP007412_testis	0.10 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_1612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1612 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2576
Pan troglodytes	retro_ptro_1505

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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,