RetrogeneDB ID: retro_pabe_3097

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:132773333..132773807(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAX
• Ensembl ID: ENSPPYG00000005911
• Aliases: None
• Description: MYC associated factor X [Source:HGNC Symbol;Acc:6913]

Sequence

>retro_pabe_3097
ATGAGTGATAATGATGACATCGAGGTGGAGAGTGACAAGCAACAACAGAGATTTCAATCTGTGGCTGACAAACGGGCCCA
TCATAATGCACTGGAATGAAATCGTAGGGACCACATCAAAGGCAGCTTTCAGTTTGTGGGACTCAGTCCCAACACTCCAA
GGAGAGAAGGCATCCTGGGCCCAAATCCTAGACAAAGCCATAGAGTATATCCAGCATATGCGAAGGGAAAAAACCACACG
CCAGTGAGATATTGATGACTTCAGCGGCAGAATGCTCTTCTGAAGCAGGAAGTCCGTGCACTGAAGGCAAGGTCAAGTGC
CCAGCCACAGGCCAACTATCCCTCCTCAGACAGCATCCTCTACACCAATGCCAAGGGCAGCACCACCTTTGCCTTTGATG
GGGGCTCCGACTACAGCTCAGAGTTGGAGCCTGAAGAACCCTGAAGTAGGAAGTAACTCCAGATGGAGGCCAGC

Alignment

ORF - retro_pabe_3097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSDNDDIEVESDEEQPRFQSAADKRAHHNALERKRRDHI-KDSFHSLRDSVPSLQGEKASRAQILDKATE
          MSDNDDIEVESD..Q.RFQS.ADKRAHHNALE..RRDHI.K..F.SL.DSVP.LQGEKAS.AQILDKA.E
Retrocopy MSDNDDIEVESDKQQQRFQSVADKRAHHNALE*NRRDHI>KAAF-SLWDSVPTLQGEKASWAQILDKAIE

Parental  YIQYMRRKNHTHQQDIDD-LKRQNALLEQQVRALEKARSSAQLQTNYPSSDNSLYTNAKGSTISAFDGGS
          YIQ.MRR...T.Q.DIDD.L.RQNALL.Q.VRAL.KARSSAQ.Q.NYPSSD..LYTNAKGST..AFDGGS
Retrocopy YIQHMRREKTTRQ*DIDD<LQRQNALLKQEVRAL-KARSSAQPQANYPSSDSILYTNAKGSTTFAFDGGS

Parental  DSSSESEPEEPQSRKKLRMEAS
          D.SSE.EPEEP.SRK.L.MEAS
Retrocopy DYSSELEPEEP*SRK*LQMEAS

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	0.06 RPM	41.14 RPM
SRP007412_cerebellum	0.00 RPM	87.67 RPM
SRP007412_heart	0.00 RPM	18.36 RPM
SRP007412_kidney	0.00 RPM	32.98 RPM
SRP007412_liver	0.00 RPM	18.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3097 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3097 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1648

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097 ,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,