RetrogeneDB ID: retro_ptro_978

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:64625571..64625865(-)
• Located in intron of: ENSPTRG00000006454

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AY
• Ensembl ID: ENSPTRG00000022504
• Aliases: None
• Description: Pan troglodytes eukaryotic translation initiation factor 1A, Y-linked (EIF1AY), mRNA. [Source:RefSeq mRNA;Acc:NM_001008977]

Sequence

>retro_ptro_978
GTATATAAAGGGGATAGACAAGAGTAGGTAATCAAAATGAAGGAAAACAGATGATTAGAATCAATGTGCTTTGATGGTGT
AAAGAGGTTATGTCATATGAGAGGAAAATTGAGAAAAAAGAAGTGAATAAATACCTCAGACATTATACTGGTTGGTCTGT
GAGACTATTAGGATAACAAATCTGATGTTATTTTAAAATACAATGCACATGAAGCTAGAAGTCTAAAGGCATATGGCAAG
TTTCTAGAATCTGCTAAAATCAATAAAACCAATATACTTGGTCCTAGAGATGAT

Alignment

ORF - retro_ptro_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFKEDGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYN
          V.K.D.QE...VIKM..N..LE..CFDGVKRLCH.RGKLRKK..INTSDIILVGL.DY.DNK.DVILKYN
Retrocopy VYKGDRQE*--VIKMKENR*LESMCFDGVKRLCHMRGKLRKKK*INTSDIILVGL*DY*DNKSDVILKYN

Parental  ADEARSLKAYGELPEHAKINETDTFGPGDD
          A.EARSLKAYG...E.AKIN.T...GP.DD
Retrocopy AHEARSLKAYGKFLESAKINKTNILGPRDD

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	0.07 RPM	7.53 RPM
SRP007412_cerebellum	0.00 RPM	3.69 RPM
SRP007412_heart	0.00 RPM	37.04 RPM
SRP007412_kidney	0.00 RPM	9.57 RPM
SRP007412_liver	0.00 RPM	5.50 RPM
SRP007412_testis	0.00 RPM	22.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_978 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_978 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1431
Gorilla gorilla	retro_ggor_1103
Pongo abelii	retro_pabe_1185
Sus scrofa	retro_sscr_948
Equus caballus	retro_ecab_634

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012660	1 retrocopy	retro_acar_151,
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Microcebus murinus	ENSMICG00000004110	2 retrocopies	retro_mmur_183, retro_mmur_197,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Nomascus leucogenys	ENSNLEG00000009913	1 retrocopy	retro_nleu_1845,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978 ,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,
Tupaia belangeri	ENSTBEG00000017492	6 retrocopies	retro_tbel_1604, retro_tbel_312, retro_tbel_3762, retro_tbel_4137, retro_tbel_4712, retro_tbel_798,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,