RetrogeneDB ID: retro_pabe_1185

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:66442037..66442344(-)
• Located in intron of: ENSPPYG00000005913

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSPPYG00000020176
• Aliases: None
• Description: Eukaryotic translation initiation factor 1A, X-chromosomal [Source:UniProtKB/Swiss-Prot;Acc:Q5RA42]

Sequence

>retro_pabe_1185
AAAGGAGAGTTGGCATATAAAGGGGATAGACAAGAGTAGGTAATCAAAATGAAGGGAAACAGATGATTAGAATCAATGTG
CTTTGATGGTGTAAAGAGGTTATGTCATATGAGAGGAAAATTGAGAAAAAAGAGGTGAATAAATACCTCAGACACTATAC
TGGTTGGTCTGTGAGACTGATCAGGATAACAAATCTGATGTTATTTTAAAATACAATGCACATGAAGCTAGAAGTCTAAA
GGCATATGGCAAGTTTCTAGAATCTGCTAAAATCAATAAAACCAATATACTTGGTCCTAGAGATGAT

Alignment

ORF - retro_pabe_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRD-YQDNKADV
          K.EL..K.D.QE...VIKM.GN..LE.MCFDGVKRLCH.RGKLRKK..INTSD.ILVGL.D..QDNK.DV
Retrocopy KGELAYKGDRQE*--VIKMKGNR*LESMCFDGVKRLCHMRGKLRKKR*INTSDTILVGL*D>DQDNKSDV

Parental  ILKYNADEARSLKAYGELPEHAKINETDTFGPGDD
          ILKYNA.EARSLKAYG...E.AKIN.T...GP.DD
Retrocopy ILKYNAHEARSLKAYGKFLESAKINKTNILGPRDD

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	64.63 RPM
SRP007412_cerebellum	0.00 RPM	110.17 RPM
SRP007412_heart	0.00 RPM	35.31 RPM
SRP007412_kidney	0.00 RPM	39.58 RPM
SRP007412_liver	0.00 RPM	28.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1185 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1185 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1431
Pan troglodytes	retro_ptro_978
Gorilla gorilla	retro_ggor_1103
Sus scrofa	retro_sscr_948
Equus caballus	retro_ecab_634

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
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,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185 ,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
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,
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,