RetrogeneDB ID: retro_ptro_2988

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390389.1:2627911..2628471(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHFR
• Ensembl ID: ENSPTRG00000017042
• Aliases: None
• Description: None

Sequence

>retro_ptro_2988
ATGGTTCATCCGCTAAACTGCATTGTCACTGTTTCCCAGAAGATGGGCATCATCAGGAATGGGGACCTGCCCTGACCCCA
GCTCAAAAATAAATTCGATTCCAAAGAATGACCACACCCTCTTCAGCAGAGGGTAAACAAAATTTAGTATTTTTTATTAG
GAAGAACTGGTTCTTGATTACTGAGAAGAATCAACCTTTAAAGTATATAATTAATTTAGTTGTCAGTAGAGAATCCAGGG
AACCACCGCAAAGACCTCCTTTTCTTGACTAAAGTCTGGGTGATGCCTTAAAACGTATTGAGCAACTAAAATCAGCAAAT
AAACAAGACGTGTTTTTTACAGTGGGAGGCAGTTCTGTTTATAAGGAATCCATGAATTGAGACCATTTTAAATTATTTGT
GACATGGATCATGCAGGACTTTCAAAGTGACACGTTTTCTCCCCTAGAAGGTGATTTAGAGAAATATAAACTTCTCCCAG
AATACCCACAAGGTGTTGTCTCTGATGTGGAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAAAAGAATGAT

Alignment

ORF - retro_ptro_2988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVGSLNCIVAVSQNMGIGKNGDLPWP-PLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLK
          MV..LNCIV.VSQ.MGI..NGDLP.P.P.....R.FQRMTT.SS.EGKQNLV....K.WF.I.EKN.PLK
Retrocopy MVHPLNCIVTVSQKMGIIRNGDLP*P<PAQK*IR-FQRMTTPSSAEGKQNLVFFIRKNWFLITEKNQPLK

Parental  GRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELASKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRI
          ..INLV.SRE..EPPQ...FL..SL.DALK..EQ...A.K.D....VGGSSVYKE.MN...H.KLFVT.I
Retrocopy YIINLVVSRESREPPQRPPFLD*SLGDALKRIEQLKSANKQDVFFTVGGSSVYKESMN-*DHFKLFVTWI

Parental  MQDFESDTFFP-EIDLEKYKLLPEYP-GVLSDVQEEKGIKYKFEVYEKND
          MQDF.SDTF.P.E.DLEKYKLLPEYP.GV.SDV.EEKGIKYKFEVYEKND
Retrocopy MQDFQSDTFSPLEGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND

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	7.83 RPM
SRP007412_cerebellum	0.00 RPM	14.45 RPM
SRP007412_heart	0.00 RPM	7.61 RPM
SRP007412_kidney	0.00 RPM	33.34 RPM
SRP007412_liver	0.00 RPM	35.65 RPM
SRP007412_testis	0.00 RPM	21.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2988 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2988 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3602
Gorilla gorilla	retro_ggor_2429
Callithrix jacchus	retro_cjac_2446

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015750	2 retrocopies	retro_amel_218, retro_amel_842,
Bos taurus	ENSBTAG00000007681	1 retrocopy	retro_btau_351,
Callithrix jacchus	ENSCJAG00000019556	4 retrocopies	retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus	ENSECAG00000026827	1 retrocopy	retro_ecab_513,
Felis catus	ENSFCAG00000026745	3 retrocopies	retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens	ENSG00000228716	4 retrocopies	retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla	ENSGGOG00000022366	2 retrocopies	retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus	ENSMLUG00000012200	2 retrocopies	retro_mluc_1109, retro_mluc_2577,
Macaca mulatta	ENSMMUG00000018283	13 retrocopies	retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica	ENSMODG00000024860	3 retrocopies	retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furo	ENSMPUG00000008704	1 retrocopy	retro_mputfur_1107,
Mus musculus	ENSMUSG00000021707	1 retrocopy	retro_mmus_3326,
Nomascus leucogenys	ENSNLEG00000012989	3 retrocopies	retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus	ENSOCUG00000005127	3 retrocopies	retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii	ENSOGAG00000025320	1 retrocopy	retro_ogar_222,
Pongo abelii	ENSPPYG00000015600	2 retrocopies	retro_pabe_2959, retro_pabe_41,
Pan troglodytes	ENSPTRG00000017042	3 retrocopies	retro_ptro_109, retro_ptro_1551, retro_ptro_2988 ,
Rattus norvegicus	ENSRNOG00000013521	1 retrocopy	retro_rnor_2030,
Sus scrofa	ENSSSCG00000014125	2 retrocopies	retro_sscr_104, retro_sscr_1131,