RetrogeneDB ID: retro_pabe_3059

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:46465934..46466761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSPPYG00000004238
• Aliases: None
• Description: Adaptin ear-binding coat-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R630]

Sequence

>retro_pabe_3059
ATGGTGGCCGAGTTGGAGTATGAGTCTGTGCTGTGTGTGAAGCCGGATGTCAGCGTCTGCTGGATTCCTCCCTGGGCCTC
CAACCATGGTTACAGGGCATCTGACTGGAAATTAGACCAGCCTGATTGGACTGGTCGCCTCCGAATCATTTCAAAAGGGA
AGACTGCCTATATCAAACTCGAGGATAAAGTTTCAAGGGAGCTCTTCACTCAGGCACCAGTAGAACAATATCCTGGTATT
GCTGTGGAGACAGTGACAGATTCCAGCTGCTACTTTTTAATCTGGATTCAGGATGGTGCTGGGCACAGTGCTGTCATTGA
CACTGCTGGCTTCACAGATAAGGAAGATGCCTTTGACTTTAATGTCTCCTTGCAGGATCACTTCAAATGGGTAAAGCAGG
AATCTGAGATTTCCAAGGAATCTCAAGAAATGGATGCTCATCCTAACTTGGATCTGGGCTTCAAAGAAGGACAAACCATC
AAGTTGAGTACAGGGAACATTACAACCAAGAAAGGAGGTGCTTCTAAGCCCAGGACTGCAATGGGTGGGGGCCTGAGCTT
ACACCCATCCCCGCCAGGAGGCAAAGTCACTATTTCCCCACTGTCCTCCTCAGTTCCATCAGCAATCATGTCACCCCACC
ACCCATTCCAAAATCTAACCATGGAGGCAGTGAAGCAGATATCCTTTTAGATTTGGATTCTCCTGCTCCTGTCACAACAC
CAGCACCAACTCCAGTTTCTGCAAGCAATGACTTGTGGGGAGACTTCAGCACTGCATCCAGCTCTGTTCCAAACCAGGCG
CCACAGCCATCCAACTGGGTCCAGTTC

Alignment

ORF - retro_pabe_3059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAELEYESVLCVKPDVSVYRIPPRASNRGYRASDWKLDQPDWTGRLRITSKGKTAYIKLEDKVSGELFA
          M.AELEYESVLCVKPDVSV..IPP.ASN.GYRASDWKLDQPDWTGRLRI.SKGKTAYIKLEDKVS.ELF.
Retrocopy MVAELEYESVLCVKPDVSVCWIPPWASNHGYRASDWKLDQPDWTGRLRIISKGKTAYIKLEDKVSRELFT

Parental  QAPVEQYPGIAVETVTDSSRYFVIRIQDGTGRSAFIG-IGFTDRGDAFDFNVSLQDHFKWVKQESEISKE
          QAPVEQYPGIAVETVTDSS.YF.I.IQDG.G.SA.I...GFTD..DAFDFNVSLQDHFKWVKQESEISKE
Retrocopy QAPVEQYPGIAVETVTDSSCYFLIWIQDGAGHSAVIDTAGFTDKEDAFDFNVSLQDHFKWVKQESEISKE

Parental  SQEMDARPKLDLGFKEGQTIKLSIGNITNKKGGASKPRTARGGGLSLLPPPPGGKVTIPPPSSSV-AISN
          SQEMDA.P.LDLGFKEGQTIKLS.GNIT.KKGGASKPRTA.GGGLSL.P.PPGGKVTI.P.SSSV..ISN
Retrocopy SQEMDAHPNLDLGFKEGQTIKLSTGNITTKKGGASKPRTAMGGGLSLHPSPPGGKVTISPLSSSV<SISN

Parental  HVTPPPIPKSNHGGSDADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF
          HVTPPPIPKSNHGGS.ADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF
Retrocopy HVTPPPIPKSNHGGSEADILLDLDSPAPVTTPAPTPVSASNDLWGDFSTASSSVPNQAPQPSNWVQF

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	0.22 RPM	107.26 RPM
SRP007412_cerebellum	0.00 RPM	117.71 RPM
SRP007412_heart	0.00 RPM	7.74 RPM
SRP007412_kidney	0.00 RPM	16.18 RPM
SRP007412_liver	0.00 RPM	15.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3059 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3059 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3839
Pan troglodytes	retro_ptro_2615

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059 ,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,