RetrogeneDB ID: retro_ggor_1271

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:58812019..58812937(-)
• Located in intron of: ENSGGOG00000000145

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_1271
TCCATGCAGTTCAGCAAGGGCCCCTCATACTGGCTCTCGGCCGAAGTCAAGAACCGGCTCCTGTCCAAATATGACCCCCA
GAAGGAGGCAGAGCTCCACAGCTGGATCGAGGGACTCACCAGCCTTTCCATCAGCCCTGACTTCCAGAAGGGCCTGAAGG
ACAGAATTATCTTACACACACTCATGAACGAGCTGCAGCCAGGCTCAGTCCCCTAGATCAACCACTCCATGCAGAACTGG
CACCAGCTAGAAAACCTCTCCAACTTCATCAAGGCCATAGTCAGCTATGGCATGAACCCCATGGACCTGTTTGAGGCCAG
TAACCTGTTTGAGAGTGGGAACATGATGCAGGTGCAGGTGTCTCTTCTTGCCCTGGCGGGGAAGGCCAAGACTAAGGGGC
TGCAGAGCGGGGTGACATCAGTGTCAGGTACTCAAAGAAGCAGCAGCGGACTTCGACTAGAACACCACGAAGGCCGGCCA
GTGCGTCATCGGGCTGCAGATGGGCACCAACAAATGTGCTAGCCAGTCAGGTATGACCATGTACGGCACAAGGAGGCATC
TCTACAGCCCCAAGAACCACATCCTGCCCCCGTGGACCACTCGACCATCAGCCTCCAGATGGGTACAAACAAGTGCGCCA
GCCACGTGGGCATGACGGCTCCCTGGACCCAGCTGCACATCTATGACACCAAGCTGGGCACCAACAAGTGTGACAACTCC
TCCGTGTCCCTGCAGATGGGCTACCTGCAGGGTGCTAACCAGAGCAGCCAGGTCTTTGGCCTGGGCCGGCAGATATACAA
TTCCAAGTACTGCCCACAAGGCCCAGCAGCCAACAGGGCTCCCTCGGGCACCAACGACCGCCCAGGCCCAGGGAAGGCCC
CTGAATATCCCCCTTACTACCAGGAGGAGGCCAGCTAC

Alignment

ORF - retro_ggor_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRTWIEGLTGLSIGPDFQKGLKDGTILCTLMNKLQPGSI
          S.QF.KGPSY.LSAEVKNRLLSKYDPQKEAEL..WIEGLT.LSI.PDFQKGLKD..IL.TLMN.LQPGS.
Retrocopy SMQFSKGPSYWLSAEVKNRLLSKYDPQKEAELHSWIEGLTSLSISPDFQKGLKDRIILHTLMNELQPGSV

Parental  PKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTKGLQSGV-D
          P.IN.SMQNWHQLENLSNFIKA.VSYGMNP.DLFEA..LFESGNM.QVQVSLLALAGKAKTKGLQSGV.D
Retrocopy P*INHSMQNWHQLENLSNFIKAIVSYGMNPMDLFEASNLFESGNMMQVQVSLLALAGKAKTKGLQSGV<D

Parental  IGVKYSEKQER-NFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILP-PMDHSTISLQ
          I.V.YS.KQ.R..FD..T.KAGQCVIGLQMGTNKCASQSGMT.YGTRRHLY.PKNHILP.P.DHSTISLQ
Retrocopy ISVRYSKKQQR<DFD*NTTKAGQCVIGLQMGTNKCASQSGMTMYGTRRHLYSPKNHILP<PVDHSTISLQ

Parental  MGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGTV
          MGTNKCAS.VGMTAP.T..HIYDTKLGT.KCDNSS.SLQMGY.QGANQS.QVFGLGRQIY..KYCPQG..
Retrocopy MGTNKCASHVGMTAPWTQLHIYDTKLGTNKCDNSSVSLQMGYLQGANQSSQVFGLGRQIYNSKYCPQGPA

Parental  ADGAPSGTGDCPDPGEVPEYPPYYQEEAGY
          A..APSGT.D.P.PG..PEYPPYYQEEA.Y
Retrocopy ANRAPSGTNDRPGPGKAPEYPPYYQEEASY

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	0.12 RPM	5.12 RPM
SRP007412_heart	0.00 RPM	32.30 RPM
SRP007412_kidney	0.12 RPM	44.49 RPM
SRP007412_liver	0.03 RPM	54.07 RPM
SRP007412_testis	0.21 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_1271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1271 has 0 orthologous retrocopies within eutheria group .

---

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,