RetrogeneDB ID: retro_pabe_3501

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:103502876..103503703(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSPPYG00000008569
• Aliases: None
• Description: importin subunit alpha-2 [Source:RefSeq peptide;Acc:NP_001126759]

Sequence

>retro_pabe_3501
GACAACTTAATCTGGGCTGGTTTGATTCCAAAATTTGTGTCTTTCTTAGGCAGAACTGATTATAGTCCCATTCAGTTTGA
ATCTGCCTGGGCGCTCACTAACGTTGCTTCTGGGAATCAGAACAAGCCAAGGTTGTGGTAGATGGAGGTGCCATCCTAGC
ATTCGTTTCTCTGTTGGCATCTCCCCATGCTCACGTCAGTGAACAAGTTGTATCGGCTCCAGGAAACATTGCACGTGATA
GCTCAGTTTTCCGAGACTTGGTTACTAAGTACAGTGCCGTTGACCCACTGTTGGTTCTTGTTGCAGTTCCTGATATGTCA
TCTTTAGCATGTGGTTACTTACGTAATCTTACCTGGACACTTTCAAATCTTTGCTGCAACAAGAATCCTGCACCCCCGTT
AGATGCTGTTGAGGAAATTCTTCCTATCTGAGTTCGGCTCCCGCATCATGATGATCCAGAAGTATTAGCAGATACCTGCT
GGGCTATTTCCTACCTGACTGATGGTCCAAATGAATGAATTGACATCGTCATGGAAACAGGAGTTGTGCCCCAACTTGTG
AAGCTTCTAGGAGCTTCTGAATTGCCAATTGTGACTCCTGCACTAAGAGCCATAGGGAATATTGTCACTGGTACAGATGA
ACGGACTCAGGTTGTGATCGATGCAGGAGCGCTTGCTGTCTTTCCCAGCCTGCTCACCAACCCCAAAACTAACACTTGGA
AGGAAGCTACATGGACAATGTCAAACATCATAGCTGGCCGTCAGGACCAGATACAGCAAGTTGTGAATCATGGATTAGTC
CTATTCCTTGCCAATGTTCTAAGTCAG

Alignment

ORF - retro_pabe_3501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGT-SEQTKAVVDGGAIPAFISLLASPHAHISEQ
          DN.I.AGLIPKFVSFLGRTD.SPIQFESAWALTN.ASG..SEQ.K.VVDGGAI.AF.SLLASPHAH.SEQ
Retrocopy DNLIWAGLIPKFVSFLGRTDYSPIQFESAWALTNVASGN<SEQAKVVVDGGAILAFVSLLASPHAHVSEQ

Parental  AVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIEAVEQ
          .V.A.GNIA.D.SVFRDLV.KY.AVDPLL.L.AVPDMSSLACGYLRNLTWTLSNLC.NKNPAPP..AVE.
Retrocopy VVSAPGNIARDSSVFRDLVTKYSAVDPLLVLVAVPDMSSLACGYLRNLTWTLSNLCCNKNPAPPLDAVEE

Parental  ILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMIVKTGVVPQLVKLLGASELPIVTPALRAIGNIV
          ILP..VRL.HHDDPEVLADTCWAISYLTDGPNE.I.....TGVVPQLVKLLGASELPIVTPALRAIGNIV
Retrocopy ILPI*VRLPHHDDPEVLADTCWAISYLTDGPNE*IDIVMETGVVPQLVKLLGASELPIVTPALRAIGNIV

Parental  TGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSK
          TGTDE.TQVVIDAGALAVFPSLLTNPKTN..KEATWTMSNI.AGRQDQIQQVVNHGLV.FL..VLS.
Retrocopy TGTDERTQVVIDAGALAVFPSLLTNPKTNTWKEATWTMSNIIAGRQDQIQQVVNHGLVLFLANVLSQ

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	17.75 RPM
SRP007412_cerebellum	0.00 RPM	11.67 RPM
SRP007412_heart	0.00 RPM	8.43 RPM
SRP007412_kidney	0.00 RPM	8.78 RPM
SRP007412_liver	0.00 RPM	11.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3501 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3501 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1140

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501 ,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Tupaia belangeri	ENSTBEG00000006274	14 retrocopies	retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,