RetrogeneDB ID: retro_pabe_85

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:106757810..106758272(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020614
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NCBP2
• Ensembl ID: ENSPPYG00000014449
• Aliases: None
• Description: nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659]

Sequence

>retro_pabe_85
ATGTCCAAAGACCTGAAAATTCTGTGTAAAGATCCTGCTTTGGAGCTGAGCTGCTACCGGGACCATCAGTTCAGTGGCAG
TAAATTTCAGCAGGAAAAATTACTGAAGGAAAGCTCCACACTGAATATGGGGAATCTTTCCTTTTATACAACCGAAGAGA
AAATACATGAGCTCTTTAGTAGATCTGATATCAGGAATATCTTTATGGGCCTGGATAAAATAAAGAAAACAGCATGTGGT
TTTTGCTTTGTAGAATGCCATAACAGAGCTGATGCTGAAAATGCCATGTGGTTTCTAACTGGGACCTGCCTAGATGAGTG
GATTATCCGCACTGATTGGGATATAGGTTTTAGAGAGGGTCAACAGTATGGTCACGGTAAATCTGAGGGTCAGGTAAGGG
ATGAGTTTCGTGAAGATTTTCATTCTGGTAGAGGAGGCTTTGGAAGACAGACTCAGATCTAG

Alignment

ORF - retro_pabe_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.77 %
• Parental protein coverage: 79.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK
          LK.L..D...ELS.YRD..F.G....QEKLLK.S.TL..GNLSFYTTEE.I.ELFS.S.DI..I.MGLDK
Retrocopy LKILCKDPALELSCYRDHQFSGSKFQQEKLLKESSTLNMGNLSFYTTEEKIHELFSRS-DIRNIFMGLDK

Parental  MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAG
          .KKTACGFCFVE...RADAENAM....GT.LD..IIRTDWD.GF.EG.QYG.G.S.GQVRDE.R.D...G
Retrocopy IKKTACGFCFVECHNRADAENAMWFLTGTCLDEWIIRTDWDIGFREGQQYGHGKSEGQVRDEFREDFHSG

Parental  RGGYGKLAQ
          RGG.G...Q
Retrocopy RGGFGRQTQ

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	11.00 RPM
SRP007412_cerebellum	0.24 RPM	8.63 RPM
SRP007412_heart	0.03 RPM	6.08 RPM
SRP007412_kidney	0.00 RPM	15.15 RPM
SRP007412_liver	0.09 RPM	8.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_85 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_85 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_85 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_5
Pan troglodytes	retro_ptro_3151
Oryctolagus cuniculus	retro_ocun_1887
Bos taurus	retro_btau_1819
Canis familiaris	retro_cfam_152
Equus caballus	retro_ecab_79

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003664	2 retrocopies	retro_amel_113, retro_amel_62,
Bos taurus	ENSBTAG00000008873	1 retrocopy	retro_btau_1819,
Canis familiaris	ENSCAFG00000013100	2 retrocopies	retro_cfam_152, retro_cfam_2195,
Callithrix jacchus	ENSCJAG00000013735	2 retrocopies	retro_cjac_3139, retro_cjac_4103,
Cavia porcellus	ENSCPOG00000002976	1 retrocopy	retro_cpor_611,
Equus caballus	ENSECAG00000016153	1 retrocopy	retro_ecab_79,
Felis catus	ENSFCAG00000029865	2 retrocopies	retro_fcat_1936, retro_fcat_561,
Homo sapiens	ENSG00000114503	1 retrocopy	retro_hsap_5,
Loxodonta africana	ENSLAFG00000006372	1 retrocopy	retro_lafr_129,
Macropus eugenii	ENSMEUG00000004730	1 retrocopy	retro_meug_34,
Microcebus murinus	ENSMICG00000003162	1 retrocopy	retro_mmur_488,
Myotis lucifugus	ENSMLUG00000017500	2 retrocopies	retro_mluc_355, retro_mluc_592,
Mustela putorius furo	ENSMPUG00000003806	1 retrocopy	retro_mputfur_9,
Mus musculus	ENSMUSG00000022774	2 retrocopies	retro_mmus_2381, retro_mmus_2645,
Nomascus leucogenys	ENSNLEG00000001727	1 retrocopy	retro_nleu_1239,
Oryctolagus cuniculus	ENSOCUG00000006738	2 retrocopies	retro_ocun_1887, retro_ocun_833,
Otolemur garnettii	ENSOGAG00000005009	6 retrocopies	retro_ogar_3151, retro_ogar_3152, retro_ogar_3153, retro_ogar_3160, retro_ogar_3161, retro_ogar_3162,
Pongo abelii	ENSPPYG00000014449	1 retrocopy	retro_pabe_85 ,
Pan troglodytes	ENSPTRG00000015789	1 retrocopy	retro_ptro_3151,
Pteropus vampyrus	ENSPVAG00000017273	3 retrocopies	retro_pvam_238, retro_pvam_305, retro_pvam_939,
Sarcophilus harrisii	ENSSHAG00000004363	2 retrocopies	retro_shar_161, retro_shar_46,
Tupaia belangeri	ENSTBEG00000015222	3 retrocopies	retro_tbel_2153, retro_tbel_3367, retro_tbel_758,
Tarsius syrichta	ENSTSYG00000014263	1 retrocopy	retro_tsyr_2008,
Tursiops truncatus	ENSTTRG00000013908	2 retrocopies	retro_ttru_442, retro_ttru_826,
Vicugna pacos	ENSVPAG00000010369	1 retrocopy	retro_vpac_493,