RetrogeneDB ID: retro_pabe_878

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:106098100..106099042(+)
• Located in intron of: ENSPPYG00000004893

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSPPYG00000002712
• Aliases: None
• Description: non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]

Sequence

>retro_pabe_878
TCTGGGGAGGCCGACATAGACCGAAAGCTCCTGGAGCTCACCGCTGACGAGGAGAAGTGCCGCAGCATCCGCAGGCAGTA
CCGACAGCTCATGTACTGCGTGCGGCAGAACCGGGAGGACATCGTGAGCTCGGAGAACAACTCCTTAACCGAGGCTCTGG
AGGAAGCCAACGTCCTGTTTGATGGCGTGAGCCGAACCAGAGAAGCAGCCCTCGACGCCCAGTTTCTTGTTATGGCTTCT
GATTTGGGTAAAGAAAAGGCAAAGCAGTTAAACTCAGATATGAACTTCTTCAATCAGTTAGCATTTTGTGACTTTCTGTT
TCTGTTCGTGGGTCTGAATTGGATGGAAGGCGATCCTGACAAGTTGAGTGATGGTGATGATAGCATAGCTCTTCCCTTCT
GGAAGGCAATAGAAAAGGAAGCAACATCCTGGATGGTAAAAGCTGAGACATTCCATTTTTTTTTTGGTTCATTCAAGCTA
GAACCTTCTGCACCAAAGCCCCGACTTGAACACCAGAAAAAAGTTCGCAAGATGGAAGAAAATGGGAACATGCCCACAAA
GTTGCGGAAGCTGGACCTGAGTAGTTATCCAGAAGCGACAGAAAAAAACATAGAAAGGATTTTGGGATTGTTGCAAACGT
ACTTTCGAAAGTATCCTGATACTCCTGTGTCCTATTTTGAGTTTGTGATTGATCCAAACTCTTTTTCTCGTACTGTGGAG
AATATATTTTATGTTTCTTTTATTGTAAGAGATGGTTTTGCAAGAATAAGGCTTGATGAAGACAGGCTGCCAATATTAGA
GCCGATGAATGTTAACCAAATGGGTGAGGGAAATGATTCCAGTTGCCATGGCAGGAAACAGGGAGTTATATCTTTGACTT
TACAGGAGTGGAAAAACATTGTGGCAGCTTTTGAAATTTCTGAGGCTATGATTACATACTCC

Alignment

ORF - retro_pabe_878 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.05 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGDEMMDPASLEAEADQGLCRQIRHQYRALINSVQQNREDILNA-GDKLTEVLEEANTLFNEVSRAREAV
          SG....D...LE..AD...CR.IR.QYR.L...V.QNREDI.......LTE.LEEAN.LF..VSR.REA.
Retrocopy SGEADIDRKLLELTADEEKCRSIRRQYRQLMYCVRQNREDIVSSENNSLTEALEEANVLFDGVSRTREAA

Parental  LDAHFLVLASDLGKEKAKQLRSDLSSFDMLRYVETLLTHMGVNPLEAEELIRDEDSPDFEFIVYDSWKIS
          LDA.FLV.ASDLGKEKAKQL.SD...F..L.....L....G.N..E......D..S.....I....WK..
Retrocopy LDAQFLVMASDLGKEKAKQLNSDMNFFNQLAFCDFLFLFVGLNWMEGDP---DKLSDGDDSIALPFWKAI

Parental  GKTAENTFNKTHTFHFLLGSIYGECPVPKPRVDRPRKVPVIQEERAMPAQLRRME-ESHQEATEKEVERI
          .K.A.....K..TF....GS...E...PKPR.....KV....E...MP..LR.....S..EATEK..ERI
Retrocopy EKEATSWMVKAETFXXXXGSFKLEPSAPKPRLEHQKKVRKMEENGNMPTKLRKLDLSSYPEATEKNIERI

Parental  LGLLQTYFREDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPIIEPVSINEENEG
          LGLLQTYFR..PDTP.S.F.FV.DP.SF.RTVENIF.VSFI.RDGFARIRLD.DRLPI.EP...N...EG
Retrocopy LGLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIVRDGFARIRLDEDRLPILEPMNVNQMGEG

Parental  FEHNTQVRNQGIIALSYRDWEEIVKTFEISEPVITPS
          .......R.QG.I.L....W..IV..FEISE..IT.S
Retrocopy NDSSCHGRKQGVISLTLQEWKNIVAAFEISEAMITYS

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	1.05 RPM	5.25 RPM
SRP007412_cerebellum	1.82 RPM	14.23 RPM
SRP007412_heart	0.60 RPM	7.59 RPM
SRP007412_kidney	0.66 RPM	11.04 RPM
SRP007412_liver	0.37 RPM	10.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_878 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878 ,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,