RetrogeneDB ID: retro_ggor_2352

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:71285645..71286830(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027912
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSGGOG00000016901
• Aliases: None
• Description: None

Sequence

>retro_ggor_2352
CTACAGTCGTAGGCCTTCCTACAGTCGTAGGCCATGTAGTTCTTCCGGGGCCTGGGTGGTGGCTCCGTGAGTTTTGCGGC
GGAGGTTGCCTTTCGCGCGCTCAGCATGCACTGGGGCTCCGGTGGCTGCGGCGTGTCCGTGTCCTCCGCCCGCTTCGTGT
CTGTCCTCGTCCTCCTTAGGGGGCTACGGCGGCGTCTTGGCCGCGTCCCACGGGCTGCTGGCGGGCAACGAGAAGCTCAA
TATGCAGAACCTCAGCGACCCTCCGGCCTCCTACCTGGACAAGGTGCGCGCCCTGGAGGCAGCCAACGGCGAACTGGAGG
TGAAGATCCGCCACTGGTACCAGAAGCAGGGGCTGGGCCCTCCCGTGACTACAGCCACTACTACAAGACTATCCAGGACC
TGCGGGACAAGATTCTTGGTGCCACCATTGAGAACTCCAGGATTGTCCTGGAGATCGACAACGCCCGTCTGGCTGCAGAT
GACTTCCGAACCAAGATTGAGACGGAGCAGGCTCTGCGCATGAGCGCGGAGGCCGACATCAACGGCCTGCGCAGGGTGCT
GGACGAGCTGACCCTGGCCATTACCGACCTGGAGATGCAGATCGAAGGCCTGAAGGAAGAGTTGGCCTACCCGAAGAAGA
ACCATGAGAAGGAAATCAGTGGGCTGAGGGGCCAAGTGGGAGGCCAGGTCAGTGGGGAGGTGGATTCGGCTCAGGGCACC
GATCTCGCCAAGATCCTGAGTGACATGCGAAGCCAATACGAGGTCATGGCGGAGCAGAACTGGAAGGATGCTGAAGCCTG
GTTCACCAGCCGGACTGAAGAATTGAACCAGGAGGTCGCTGGCCACACAGATCAGCTCCAGATGAGCCGGTCCAAGGTCA
CTGACCTGCAGCGTACCCTCCAGGGTCTTGAGCTGCAGTCACGGCTGAGCATGAAAGCCGCCTTGGAAGGCACACTGGCA
GAAACGGAGGCGCGCTTTGGAGTCCAGCTGGCGCAGATCCATCCGCTGATCAACTGCATTGAAGCCCAGCTGGGCGATGT
GCGAGCTGATAGTGAGCGGCAGAATCAGGATTACCAGCAGTTCGTGGACATCAAGTCGCGGCTGGAGCAGGAGATCTCCA
CCTACCGCAGCCTGCTCGAGGGCCAGAAAGATCACTACAACAACCTGTCCGCCTCCAAGGTCCTC

Alignment

ORF - retro_ggor_2352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTSYSYRQSSATSSFGGLGGGSVRFGPGVAFRAPSIHGGSGGRGVSVSSARFVS-SSSSGGYGGGYGGVL
          ..S....QS.A...F.GLGGGSV.F...VAFRA.S.H.GSGG.GVSVSSARFVS.SSSS.G...GYGGVL
Retrocopy LQS*AFLQS*AM*FFRGLGGGSVSFAAEVAFRALSMHWGSGGCGVSVSSARFVS>SSSSLG---GYGGVL

Parental  TASDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQ-GPGPSRDYSHYYTTIQDLR
          .AS.GLLAGNEKL.MQNL.D..ASYLDKVRALEAANGELEVKIR.WYQKQ.G.GPSRDYSHYY.TIQDLR
Retrocopy AASHGLLAGNEKLNMQNLSDPPASYLDKVRALEAANGELEVKIRHWYQKQ<GAGPSRDYSHYYKTIQDLR

Parental  DKILGATIENSRIVLQIDNARLAADDFRTKFETEQALRMSVEADINGLRRVLDELTLARTDLEMQIEGLK
          DKILGATIENSRIVL.IDNARLAADDFRTK.ETEQALRMS.EADINGLRRVLDELTLA.TDLEMQIEGLK
Retrocopy DKILGATIENSRIVLEIDNARLAADDFRTKIETEQALRMSAEADINGLRRVLDELTLAITDLEMQIEGLK

Parental  EELAYLKKNHEEEISTLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSRTEEL
          EELAY.KKNHE.EIS.LRGQVGGQVS.EVDSA.GTDLAKILSDMRSQYEVMAEQN.KDAEAWFTSRTEEL
Retrocopy EELAYPKKNHEKEISGLRGQVGGQVSGEVDSAQGTDLAKILSDMRSQYEVMAEQNWKDAEAWFTSRTEEL

Parental  NREVAGHTEQLQMSRSEVTDLRRTLQGLEIELQSQLSMKAALEDTLAETEARFGAQLAHIQALISSIEAQ
          N.EVAGHT.QLQMSRS.VTDL.RTLQGL..ELQS.LSMKAALE.TLAETEARFG.QLA.I..LI..IEAQ
Retrocopy NQEVAGHTDQLQMSRSKVTDLQRTLQGL--ELQSRLSMKAALEGTLAETEARFGVQLAQIHPLINCIEAQ

Parental  LGDVRADSERQNQEYQRLMDIKSRLEQEIATYRSLLEGQEDHYNNLSASKVL
          LGDVRADSERQNQ.YQ...DIKSRLEQEI.TYRSLLEGQ.DHYNNLSASKVL
Retrocopy LGDVRADSERQNQDYQQFVDIKSRLEQEISTYRSLLEGQKDHYNNLSASKVL

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	1.20 RPM
SRP007412_cerebellum	0.00 RPM	6.97 RPM
SRP007412_heart	0.03 RPM	1.72 RPM
SRP007412_kidney	0.00 RPM	45.75 RPM
SRP007412_liver	0.00 RPM	6.70 RPM
SRP007412_testis	19.17 RPM	8.08 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_2352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2352 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3486
Pan troglodytes	retro_ptro_2359
Pongo abelii	retro_pabe_2880
Macaca mulatta	retro_mmul_1770

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352 , retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,