RetrogeneDB ID: retro_pabe_3682

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:108540220..108541502(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFN1
• Ensembl ID: ENSPPYG00000014318
• Aliases: None
• Description: mitofusin 1 [Source:HGNC Symbol;Acc:18262]

Sequence

>retro_pabe_3682
CAAGATTACAGGAATTTCAGAATTTTGAACAAATCTTTGAGGAGTGTATCTCACAGTCAGCAGTGAAAACAGTTTGAACA
GCACACTATCAGAGCTAAACAGATACTAGCTACTGTGAAAAAACAATGGATTCAATAAACATGGCAGCTGAACAGAAAAG
GCATTATGCAGTGGAAGAGAAGGAAGACCAAACTGATAGACTGGACTTTATCTGAAACCAGATGAACCTTTTAACACTGG
ATGTTAAGAAAAAAACCAAGGAGGTTACTGGGGAGGTGGCAAACAAAGTGTCATGTGCAATGACAGATGAAATTTGTCGA
CTGTCTGTTTTGGTTGATGAATTTTGTTCAGAGTTTCATCCTACTCCAGATGTATTAAAAATATATAAAAGTGAATTAAA
TAAGCATATAGAGGATGGTATGGGAAGAAATTTGGCTGATCGATGCACCAATGAAGTAAACACCTAGTGCTTCAGTTCCA
GCAAGAAATTGTTGAAAGTTTGAAGCCATTACTTCCAGCTGGTATACAGGATAAACTACATACACTGATCCCTTGCAAGA
AATTTGATCTCAGCTATAATCTAAATTACCACAAGTTATGTTCAGATTTTCAAGAGGATATTGTATTTCATTTTTCCCTG
GGCTGGTCTTCCCTCGTACCTCAATTTTTGGGCCCTAGAAATGCTCAAATGGTGCTCCTAGGATTATCAGAGCCTATCTT
TCAGCTCCCTAGATCTTTAGCTTCTACTCCCACTGCTCCTACCAGTCCAGCAATGCCAGATAATGCATCACAGGAAGAAC
TCATGATTACATTAGTAACAGGATTGGCTTCTCTTACATCTAGAACTTCTATGGGCATCAATATTGTTGGAGGAATTATT
TGGAAAACTATAGGCTGGAAACTCATATCTGTTTCATTAACTATGTATGGAGCTTTGTATCTTTATGAAAGATCATCCTG
GACCACCCATGCCAAGGAGAGAGCTTTTAAACAGCAGTTTGTTAACTATGCAACTGAAAAAATGAAGATGATTGCTAGCT
CCACAAGTGCAAACTGCAGCCACCAAGTAAAACAACAAATGGCTACCACTTTTGCTCACCTGTGCCAACAAGTTGATATT
ACTCAAAGACAACTGGAAGAAGAAATTGCTAGATTACCCAAAGAAATAGATCAGTGGGAGAAAATACAAAACAATTTAAA
GCTCTTAAGAAATAAAGCTGTTCAACTTGAAAATGAGCTGGAGAATTTTACTAAGCAGTTTCTACCTTCACGTGATGAAG
AA

Alignment

ORF - retro_pabe_3682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.74 %
• Parental protein coverage: 57.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEFQNFEQIFEEC--ISQSAVKTKFEQHTIRAKQILATVKN-IMDSVNLAAEEKRHYSVEEREDQIDRLD
          Q...NF..........S.S.....FEQHTIRAKQILATVK...MDS.N.AAE.KRHY.VEE.EDQ.DRLD
Retrocopy QDYRNFRILNKSLRSVSHSQQ*KQFEQHTIRAKQILATVKK<TMDSINMAAEQKRHYAVEEKEDQTDRLD

Parental  FIRNQMNLLTLDVKKKIKEVTEEVANKVSCAMTDEICRLSVLVDEFCSEFHPNPDVLKIYKSELNKHIED
          FI.NQMNLLTLDVKKK.KEVT.EVANKVSCAMTDEICRLSVLVDEFCSEFHP.PDVLKIYKSELNKHIED
Retrocopy FI*NQMNLLTLDVKKKTKEVTGEVANKVSCAMTDEICRLSVLVDEFCSEFHPTPDVLKIYKSELNKHIED

Parental  GMGRNLADRCTDEVNA-LVLQTQQEIIENLKPLLPAGIQDKLHTLIPCKKFDLSYNLNYHKLCSDFQEDI
          GMGRNLADRCT.EVN..LVLQ.QQEI.E.LKPLLPAGIQDKLHTLIPCKKFDLSYNLNYHKLCSDFQEDI
Retrocopy GMGRNLADRCTNEVNT<LVLQFQQEIVESLKPLLPAGIQDKLHTLIPCKKFDLSYNLNYHKLCSDFQEDI

Parental  VFRFSLGWSSLVHRFLGPRNAQRVLLGLSEPIFQLPRSLASTPTAPTTPATPDNASQEELMITLVTGLAS
          VF.FSLGWSSLV..FLGPRNAQ.VLLGLSEPIFQLPRSLASTPTAPT.PA.PDNASQEELMITLVTGLAS
Retrocopy VFHFSLGWSSLVPQFLGPRNAQMVLLGLSEPIFQLPRSLASTPTAPTSPAMPDNASQEELMITLVTGLAS

Parental  LTSRTSMGIIIVGGVIWKTIGWKLLSVSLTMYGALYLYERLSWTTHAKERAFKQQFVNYATEKLKMIVSS
          LTSRTSMGI.IVGG.IWKTIGWKL.SVSLTMYGALYLYER.SWTTHAKERAFKQQFVNYATEK.KMI.SS
Retrocopy LTSRTSMGINIVGGIIWKTIGWKLISVSLTMYGALYLYERSSWTTHAKERAFKQQFVNYATEKMKMIASS

Parental  TSANCSHQVKQQIATTFARLCQQVDITQKQLEEEIARLPKEIDQLEKIQNNSKLLRNKAVQLENELENFT
          TSANCSHQVKQQ.ATTFA.LCQQVDITQ.QLEEEIARLPKEIDQ.EKIQNN.KLLRNKAVQLENELENFT
Retrocopy TSANCSHQVKQQMATTFAHLCQQVDITQRQLEEEIARLPKEIDQWEKIQNNLKLLRNKAVQLENELENFT

Parental  KQFLPSSNEE
          KQFLPS..EE
Retrocopy KQFLPSRDEE

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	0.33 RPM	16.64 RPM
SRP007412_cerebellum	0.49 RPM	35.51 RPM
SRP007412_heart	0.15 RPM	17.31 RPM
SRP007412_kidney	0.20 RPM	11.47 RPM
SRP007412_liver	0.09 RPM	9.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3682 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013155	1 retrocopy	retro_cjac_554,
Nomascus leucogenys	ENSNLEG00000005745	1 retrocopy	retro_nleu_1240,
Pongo abelii	ENSPPYG00000014318	1 retrocopy	retro_pabe_3682 ,