RetrogeneDB ID: retro_mmul_437

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:159535612..159537516(+)
• Located in intron of: ENSMMUG00000016102

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPO7
• Ensembl ID: ENSMMUG00000023636
• Aliases: None
• Description: None

Sequence

>retro_mmul_437
GAAACACTTTGAATTGAAGAAGATGATCGACCTGAGTTACCATAGTGAAAATGCAAGAAGTGGGCCTTACATATTTTAGC
AAGACTTTTTGAAAGATATGAAAGCCCTGGCAATGTTTCCTAGGACTACAGTAAGTTGGCTGAAGTATTTCTGAAGGCAT
TTGTTGTTGGTGTCCAGCAAGTTTTATTAAAGGTGTTATAACAATACAAGGAGAAGCAATATATGTTTCCTCAAGTTTTA
CAACAGACATTAAATTCTATTAATCAAGGAGTTTCTCATGCTCTCACCTGGAAGAAACTGAAACCCCATATACAAGGCAT
TATCCAAGATGTTATTTTTCCATTGATGTGTTATACAGATGCTGATGAGGAACTTCGGGAAGAAGACCCTTACGAATATA
TAAGCATGAAGTTTAATGTGTTTGAAGATTTCATTCCTTTTACCACTGCTGCCCAGAAGCTTTTGTTTACAGCCCGTAGT
AAGAGGAAACAGGTACTTCAAAAGACTATGGGATTTTGTTACCGGATTCTTACAGAACCAAATGCTGACCTTTGAAAAAC
AGATGGAGCCCTGCATATGATTGGGTCTTGAGCTGAAATACTTCTGAAGAAGAAGATCTATAAAGATCAGATGGAATACA
TGTTGCAGAATCATGTATTCTTTTCAGCAGTGAACTAGGCTATGAGAGCAAGGGCTTGCTGGGTGCTTCACTATTTTTGT
GAAGTAAAGTTCAAAAGTGATCAGAACCTTCAGACAGCTTTAGAGCTAACAAGATGTCTGATTGATGATAGAGACATGCC
TGTGAAAGTGGAAGCTGCCATTGTCTTTCAAGTATTGATCAGCAATCAAGAAAAATTTAAAGAATATATCACACCATTCA
TCAGACCTGTAATGCAGGCTTTTCTTCATATTATAAGAGAAACAGAAAATGATGACCTTACCAATGTAATTCGGAAAATG
ATCTGTGAAAATAGCGAAGAAGTTACTCTTGTTGCAGTAGAAATGGCACAATAGTTGGCAATGACATTTAGCCAAGTAAT
CCAGATCAGTCCTGATAAAGAAGGTAGTGATGACAAAGCAGTTACTGCTATGGGAATTCTGAATACAGCTGACACACTTC
TTAGTTGTAGTTGAAGATCATAAAGAGATAACCCAACAGCTTGAGGGAATCTGCTTACAGGTCATTGGTACTGTTTTACA
ACAGCATGTCTCAGAATCCTATGAGGAGATATTCTCTTTAGCGCGTAGCCTGACATGTCAACAAGTGTCTCCACAAATGT
GGCAGCTACCACCCCTTGTATTTGAAGTCTTTCAGCAAGATGGCTTTGATTACTTTACAGATATGATGCCGCTCCTTTAT
AATTATGTAACAGTTCTTAGCAAGACATTTCTGTCTGATACCCAGTATCTTGAAATGATATACAGTATGTGCAAAAAGGT
TCTTACAGGAGTTGCAGGAGAAGATGCAGAGTGTCATGCGGCAAAATTGTTAGAGGTCATCATTCTGCAGTGCAAAGGGC
ATGACATTGACCAGTGCATTTCCTTATTCATGCAAGCAGCCTTAGAAAGACTGACAGAGGTTAAGACAAGTGAACTTTGA
ACTATATGTCTGCAAGTTGCAATTGCAGCTTTGCATTATAATGCATACCTATTACTCAATACCTTAGAAAATCTTCACTT
CCCTAATAATGTTTAACCAGTTACAAATAATTTTATTAGACAGTGGCTTAATGATGTTGACTGTTTCTTGAGGCTTCATG
ACAGAAATATGTGTGGTCTCAGTCTCTGTGCTCTTATTGATAATGGAACAGACACCCCAAGGTTTGAATCAGGTTTCTGG
ACAGATTTTGCCAGCTTTTATCCTTTTATTGAATGGATTGAAAAGAGCATATGCCTGCCATGCT

Alignment

ORF - retro_mmul_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 68.38 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETLQVEEDDRPELPWWKCKKWALHILARLFERYGSPGNVSKEYNEFAEVFLKAFAVGVQQVLLKVLYQYK
          ETL..EEDDRPELP..KCKKWALHILARLFERY.SPGNVS..Y...AEVFLKAF.VGVQQVLLKVL.QYK
Retrocopy ETL*IEEDDRPELP**KCKKWALHILARLFERYESPGNVS*DYSKLAEVFLKAFVVGVQQVLLKVL*QYK

Parental  EKQYMAPRVLQQTLNYINQGVSHALTWKNLKPHIQGIIQDVIFPLMCYTDADEELWQEDPYEYIRMKFDV
          EKQYM.P.VLQQTLN.INQGVSHALTWK.LKPHIQGIIQDVIFPLMCYTDADEEL..EDPYEYI.MKF.V
Retrocopy EKQYMFPQVLQQTLNSINQGVSHALTWKKLKPHIQGIIQDVIFPLMCYTDADEELREEDPYEYISMKFNV

Parental  FEDFISPTTAAQTLLFTACSKRKEVLQKTMGFCYQILTEPNADPRKKDGALHMIGSLAEILLKKKIYKDQ
          FEDFI..TTAAQ.LLFTA.SKRK.VLQKTMGFCY.ILTEPNAD..K.DGALHMIGS.AEILLKKKIYKDQ
Retrocopy FEDFIPFTTAAQKLLFTARSKRKQVLQKTMGFCYRILTEPNADL*KTDGALHMIGS*AEILLKKKIYKDQ

Parental  MEYMLQNHVFPLFSSELGYMRARACWVLHYFCEVKFKSDQNLQTALELTRRCLIDDREMPVKVEAAIALQ
          MEYMLQNHVF..FS.....MRARACWVLHYFCEVKFKSDQNLQTALELT.RCLIDDR.MPVKVEAAI..Q
Retrocopy MEYMLQNHVF--FSAVN*AMRARACWVLHYFCEVKFKSDQNLQTALELT-RCLIDDRDMPVKVEAAIVFQ

Parental  VLISNQEKAKEYITPFIRPVMQALLHIIRETENDDLTNVIQKMICEYSEEVTPIAVEMTQHLAMTFNQVI
          VLISNQEK.KEYITPFIRPVMQA.LHIIRETENDDLTNVI.KMICE.SEEVT..AVEM.Q.LAMTF.QVI
Retrocopy VLISNQEKFKEYITPFIRPVMQAFLHIIRETENDDLTNVIRKMICENSEEVTLVAVEMAQ*LAMTFSQVI

Parental  QTGPDEEGSDDKAVTAMGILNTIDTLLS-VVEDHKEFSFSLKGNILSVKTILTIIEEFVFSVSLELGGSF
          Q..PD.EGSDDKAVTAMGILNT.DTLLS.VVEDHKE....L.G..L.V..I.T.....V.....E.....
Retrocopy QISPDKEGSDDKAVTAMGILNTADTLLS>VVEDHKEITQQLEGICLQV--IGTVLQQHVSESYEEIFSLA

Parental  LHLSINEYILIKTEYLPFSKEIFQKQRFFINTDMMPLLHNYVTVDTDTLLSDTKYLEMIYSMCKKVLTGV
          ..L.............P...E.FQ...F...TDMMPLL.NYVTV...T.LSDT.YLEMIYSMCKKVLTGV
Retrocopy RSLTCQQVSPQMWQLPPLVFEVFQQDGFDYFTDMMPLLYNYVTVLSKTFLSDTQYLEMIYSMCKKVLTGV

Parental  AGEDAECHAAKLLEVIILQCKGRGIDQCIPLFVEAALERLTREVKTSELRTMCLQVAIAALYYNPHLLLN
          AGEDAECHAAKLLEVIILQCKG..IDQCI.LF..AALERLT.EVKTSEL.T.CLQVAIAAL.YN..LLLN
Retrocopy AGEDAECHAAKLLEVIILQCKGHDIDQCISLFMQAALERLT-EVKTSEL*TICLQVAIAALHYNAYLLLN

Parental  TLENLRFPNNVEPVTNHFITQWLNDVDCFLGLHDRKMCVLGLCALID-MEQIPQVLNQVSGQILPAFILL
          TLENL.FPNNV.PVTN.FI.QWLNDVDCFL.LHDR.MC.L.LCALID.MEQ.PQ.LNQVSGQILPAFILL
Retrocopy TLENLHFPNNV*PVTNNFIRQWLNDVDCFLRLHDRNMCGLSLCALID>MEQTPQGLNQVSGQILPAFILL

Parental  FNGLKRAYACHA
          .NGLKRAYACHA
Retrocopy LNGLKRAYACHA

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	6.39 RPM	120.79 RPM
SRP007412_brain_prefrontal_cortex	2.78 RPM	78.06 RPM
SRP007412_cerebellum	5.23 RPM	115.07 RPM
SRP007412_heart	2.89 RPM	91.10 RPM
SRP007412_kidney	3.29 RPM	73.59 RPM
SRP007412_liver	0.99 RPM	30.84 RPM
SRP007412_testis	0.57 RPM	24.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_437 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_437 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_501

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015965	1 retrocopy	retro_ecab_345,
Homo sapiens	ENSG00000205339	1 retrocopy	retro_hsap_501,
Gorilla gorilla	ENSGGOG00000002260	1 retrocopy	retro_ggor_973,
Macaca mulatta	ENSMMUG00000023636	1 retrocopy	retro_mmul_437 ,
Pongo abelii	ENSPPYG00000029652	1 retrocopy	retro_pabe_1036,