RetrogeneDB ID: retro_pabe_3769

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:63792051..63792724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR1
• Ensembl ID: ENSPPYG00000018631
• Aliases: None
• Description: Mitochondrial fission regulator 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFN3]

Sequence

>retro_pabe_3769
AAGCTTACCTGCCATGCAACAGAATCGCGTCCCAACCACCCAGGAGAGGATGCAGTGTTGTCTTTTGTGGCTGTTGAATG
GGTAGCCAAAGGAGAGTGTTCAACAAGACTAAGAACAGAGGCCAGGTCAAGGCTATCCTTTCAGGATGACCTTTTCTTTG
AGAAGGCCCCAAGCAGACAGATTTCCTTACCAGACTTGTCTCAAGAGGAGCCTCAGCTGAAGACTCCAGCCTGGTAAATG
AGGAAGCACTGCAGAAGATTTGTGCTCTTGAAAATGAATTTGCTGCTCTCAGAGCTCAGATAACCAAAATTGTGACTCAG
CAATAGCAGGAAAATCTAATTGCAAGTGACTTAGATTTTACCACATCTGTTACCACACCACCATCCCCTCCACCTCTCCC
ACCACTCTTGCCCCCCCTCTCCACTGGGACTCCACGAAAGTATATCTGATATCGATCTGATTAGAGAGTGAGGAGGGAGA
AAAGCCAATTCTGGAAAGACGTTGGTTAAGAACAATCCAAAAAAAAGCTGACATGCCAAAAATGCTAGAGATTCTTAAAG
ATATGATCAGTGTAAAACTTTAGTCAGTAAAAATTTCAGAGCAAGATGTACAGCCCAAGCCAGTGGATGCTGCTGGACCT
GCTCCCCTCATAGCAGAGTCTCTAAAAAAGAAA

Alignment

ORF - retro_pabe_3769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.74 %
• Parental protein coverage: 68.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QINSHATEWSPSHPGEDAVASFADVGWVAKEEGECSARLRTEVRSRPPLQDDLLFFEKAPSRQISLPDFS
          ....HATE..P.HPGEDAV.SF..V.WVAK..GECS.RLRTE.RSR...QDDL.FFEKAPSRQISLPD.S
Retrocopy KLTCHATESRPNHPGEDAVLSFVAVEWVAK--GECSTRLRTEARSRLSFQDDL-FFEKAPSRQISLPDLS

Parental  QEEPQLKTPA-LANEEALQKICALENELAALRAQIAKIVTQQEQQNLTAGDLDSTTFGTIPPHPLPPPP-
          QEEPQLKTPA.L.NEEALQKICALENE.AALRAQI.KIVTQQ.Q.NL.A.DLD.TT..T.PP.P.P.PP.
Retrocopy QEEPQLKTPA<LVNEEALQKICALENEFAALRAQITKIVTQQ*QENLIASDLDFTTSVTTPPSPPPLPP>

Parental  PPPPPPLGLHQSISAVDLIKERREKRANAGKTLVKNS-PKKPEMPNMLEILKDMNSVKLRSVKRSEQDVK
          ..PP.PLGLH.SIS..DLI.E.....AN.GKTLVKN.......MP.MLEILKDM.SVKL.SVK.SEQDV.
Retrocopy SCPPSPLGLHESISDIDLIRE*GGRKANSGKTLVKNN>XXXADMPKMLEILKDMISVKL*SVKISEQDVQ

Parental  PKPVDATDPAALIAEALKKK
          PKPVDA..PA.LIAE.LKKK
Retrocopy PKPVDAAGPAPLIAESLKKK

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	4.59 RPM
SRP007412_cerebellum	0.00 RPM	8.88 RPM
SRP007412_heart	0.00 RPM	11.50 RPM
SRP007412_kidney	0.00 RPM	34.27 RPM
SRP007412_liver	0.00 RPM	16.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3769 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3769 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4849
Macaca mulatta	retro_mmul_2590

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700, retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769 ,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,