RetrogeneDB ID: retro_ptro_2359

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:71889897..71891083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSPTRG00000009168
• Aliases: None
• Description: None

Sequence

>retro_ptro_2359
ATGACTTCCTACAGCTATCGCCAGTCGTAGGCCAAGTAGTCCCTCCGGAGCCTGGGTGGTGGCTCCGTGAGTTTTGCGGC
GGAGGTTGCCTTTCGCGCGCTCAGCATGCACTAGGGCTCCGGAGACTGCGGCATGTCCGTGTCCTCCGCCCGCTTCGTGT
CTGTCCTCGTCCTCCTTGGGGGGCTACGGCGGCGTCTTGGCCGCGTCCCACGGGCTGCTGGCGGGCAACGAGAAGCTCAA
TATGCAGAACCTCAGCGACCCTCTGGCCTCCTACCTGGACAAGGTGCGCGCCCTGGAGGCAGCCAACAGCGAACTGGCGG
TGAAGATCCGCGACTGGTACCAGAAGCAGGGGCCCGGGCCCTCCCGTGACTACAGCCACTACTACAAGACTATCCAGGAC
CTGCGGGACAAGATTCTTGGTGCCACCATTGAGAACTCCAGGATTGTCCTGGAGATCGACAACGCCCGTCTGGCTGCAGA
TGACTTCCAAACCAAGATTGAGACGGAGCAGGCTCTGCGCATGAGCGCGGAGGCCGACATCAACGGCCTGCGCAGGGTGC
TGGACGAGCTGACCCTGGCCATTACCGACCTGGAGATGCAGATCGAAGGCCTGAAGGAATAGCTGGCCTACCTGAAGAAG
AACCATGAGAAGGAAATCAGTGGGCTGAGGGGCCAAGTGGGAGGCCAGGTCAGTGGGGAGGTGGATTCAGCTCAGGGCAC
CGATCCCGCCAAGATCCTGAGTGACATGCGAAGCCAATACGAGGTCATGGCGGAGCAGAACTGGAAGGATACTGAAGCCT
GGTTCACCAGCCGGACTGAAGAATTGAACCGGGAGGTCGCTGGCCACACAGATCAGCTCCAGATGAGCCGGTCCAAGGTC
GCTGATCTGCGGCGCACCCTCCAGGGTCTTGAGCTGCAGTCACGGCTGAGCATGAAAGCCGCCTTGGAAGGCACACTGGC
AGAAACGGAGGTGCGCTTTGGAGTCCAGCTGGCGCAGATCCAGCCGCTGATCAACTGTATTGAAGCCCAGCTGGGCGATG
TGCGAGCTGATAGTGAGCAGCAGAATCAGGATTACCAGCAGTTCACGGACATCAAGTCGCGGCTGGAGCAGGAGATCTCC
ACCTACCGCAGCCTGCTCGAGGGCCAGAAAGATCACTACAACAACCTGTCCGCCTCCAAGGTCCTC

Alignment

ORF - retro_ptro_2359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSYSYRQSSATSSFGGLGGGSVRFGPGVAFRAPSIHGGSGGRGVSVSSARFVS-SSSSGGYGGGYGGVL
          MTSYSYRQS.A..S...LGGGSV.F...VAFRA.S.H.GSG..G.SVSSARFVS.SSSS.G...GYGGVL
Retrocopy MTSYSYRQS*AK*SLRSLGGGSVSFAAEVAFRALSMH*GSGDCGMSVSSARFVS>SSSSLG---GYGGVL

Parental  TASDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRDYSHYYTTIQDLRD
          .AS.GLLAGNEKL.MQNL.D.LASYLDKVRALEAAN.EL.VKIRDWYQKQGPGPSRDYSHYY.TIQDLRD
Retrocopy AASHGLLAGNEKLNMQNLSDPLASYLDKVRALEAANSELAVKIRDWYQKQGPGPSRDYSHYYKTIQDLRD

Parental  KILGATIENSRIVLQIDNARLAADDFRTKFETEQALRMSVEADINGLRRVLDELTLARTDLEMQIEGLKE
          KILGATIENSRIVL.IDNARLAADDF.TK.ETEQALRMS.EADINGLRRVLDELTLA.TDLEMQIEGLKE
Retrocopy KILGATIENSRIVLEIDNARLAADDFQTKIETEQALRMSAEADINGLRRVLDELTLAITDLEMQIEGLKE

Parental  ELAYLKKNHEEEINTLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSRTEELN
          .LAYLKKNHE.EI..LRGQVGGQVS.EVDSA.GTD.AKILSDMRSQYEVMAEQN.KD.EAWFTSRTEELN
Retrocopy *LAYLKKNHEKEISGLRGQVGGQVSGEVDSAQGTDPAKILSDMRSQYEVMAEQNWKDTEAWFTSRTEELN

Parental  REVAGHTEQLQMSRSEVTDLRRTLQGLEIELQSQLSMKAALEDTLAETEARFGAQLAHIQALISGIEAQL
          REVAGHT.QLQMSRS.V.DLRRTLQGL..ELQS.LSMKAALE.TLAETE.RFG.QLA.IQ.LI..IEAQL
Retrocopy REVAGHTDQLQMSRSKVADLRRTLQGL--ELQSRLSMKAALEGTLAETEVRFGVQLAQIQPLINCIEAQL

Parental  GDVRADSERQNQEYQRLMDIKSRLEQEIATYRSLLEGQEDHYNNLSASKVL
          GDVRADSE.QNQ.YQ...DIKSRLEQEI.TYRSLLEGQ.DHYNNLSASKVL
Retrocopy GDVRADSEQQNQDYQQFTDIKSRLEQEISTYRSLLEGQKDHYNNLSASKVL

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	1.63 RPM
SRP007412_cerebellum	0.00 RPM	11.33 RPM
SRP007412_heart	0.03 RPM	2.45 RPM
SRP007412_kidney	0.00 RPM	92.97 RPM
SRP007412_liver	0.00 RPM	5.53 RPM
SRP007412_testis	12.65 RPM	0.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2359 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2359 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3486
Gorilla gorilla	retro_ggor_2352
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,