RetrogeneDB ID: retro_ptro_697

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:63421815..63422715(+)
• Located in intron of: ENSPTRG00000004773

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSPTRG00000016643
• Aliases: None
• Description: None

Sequence

>retro_ptro_697
AAAATGAAGGAAGTGAAAACGAATCTGCAAAAATGAGTGCAAAAAGCCAGGAAGAAACTCAAACTCAGCGATGAATCTGA
AGAAAGTGATGTGAGAAGAAAAGTTAAGTCAGTGGAGAAAATAAAGACCCAACAACACGAGGCTATTCCAACTACAGCAT
CTTCAGCCCTTTCAGAGAAACCAGCCGACTCAGTCACTTCCAAAACCATAGGACCCATTAATGCCCAGCCATCTGCTGAA
AAAGACACGCTGACAACAGAAAGTCAAGCAAAACCCAGAAAAAAGGGAATACATCTTATGGCAAAAGGAAGAAATCAAGA
AGTGAAGCAACAGACTCAGATATTTCCAACATTGTGCATATTTGGTGTCTGGAAGGAAAGAAAACCAATGACATCATGGA
ATTGAATATTGTTTTGCCTGCATTTGAGAAAACCCTCGTCCAGTATAAACATAGAATAGAATCTAAAATTTGTAAGAAAC
ACATCAATAAATTTTATTTTACTAGTAAAGAAGAACTCAACAAAATGCTTAAAAAGTCCAGATATTGAAAAATCTGAAAA
AGAAGAATGCTAAGGTAATTTCAGATATCAAAAAGAAATGACAGCGTTTGACTGAAGTCCAGGATGAGCTGCTTTGGTTA
GAGCCACCAACTGAAACAACTACAAACAAAATATTATGAACTTAAGGAGAGAACAGTCTTCCCTTAGGAATGCAGCTATT
TCTTATCTAATTCAAAACAACTCCATCGGAAGTATTCAGATGTTCAGGAGAAAGAACCAAACGTAAAGGAAACATAAGAT
TCATCCAGCCTTCCAGGTGTTATTTAAAGTAGGAACACTTTTGGGAGCTGAAAATCTTCTGTGAAATATCAGCCATCAAT
GAGAGAAGCTCCTCCACCAG

Alignment

ORF - retro_ptro_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.84 %
• Parental protein coverage: 71.5 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EIESVKISAKKPGRMLRPISDDSESIEESDTRIKVKSAEKINTQRHEVIRTTASSELSEKPAESVTSKKT
          ....VK....K.....R.....S...EESD.R.KVKS.EKI.TQ.HE.I.TTASS.LSEKPA.SVTSK..
Retrocopy KMKEVKTNLQK*VQKARKKLKLSDESEESDVRRKVKSVEKIKTQQHEAIPTTASSALSEKPADSVTSKTI

Parental  GPLSAQPSVEKENLAIESQ-SKTQKKGKMSHDKRKKSRSKAVGSDTSDIVHIWCPEGMKTSDIKELNIVL
          GP..AQPS.EK..L..ESQ.SKTQKKG..S..KRKKSRS.A..SD.S.IVHIWC.EG.KT.DI.ELNIVL
Retrocopy GPINAQPSAEKDTLTTESQ<SKTQKKGNTSYGKRKKSRSEATDSDISNIVHIWCLEGKKTNDIMELNIVL

Parental  PEFEKTHLEHQQRIESKVCKAAIATFYVNVKEQFIKMLKES-QMLTNLKRKNAKMISDIEKKRQRMIEVQ
          P.FEKT......RIESK.CK..I..FY...KE...KMLK.S.Q.L.NLK.KNAK.ISDI.KK.QR..EVQ
Retrocopy PAFEKTLVQYKHRIESKICKKHINKFYFTSKEELNKMLKKS<QILKNLKKKNAKVISDIKKK*QRLTEVQ

Parental  DELLRLEP-QLKQLQTKYDELKER-KSSLRNAA-YFLSNLKQLYQDYSDVQAQEPNVKETYDSSSLPALL
          DELL.LEP.QLKQLQTKY.ELKER..SSLRNAA.YFLSN.KQL...YSDVQ..EPNVKET.DSSSLP...
Retrocopy DELLWLEP>QLKQLQTKYYELKER>QSSLRNAA<YFLSNSKQLHRKYSDVQEKEPNVKET*DSSSLPGVI

Parental  FKARTLLGA-ESHLRNINHQLEKLLDQ
          ...R...G..E..L.NI.HQ.EKLL.Q
Retrocopy -*SRNTFGS>ENLL*NISHQ*EKLLHQ

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	0.04 RPM	0.70 RPM
SRP007412_cerebellum	0.00 RPM	1.86 RPM
SRP007412_heart	0.00 RPM	1.17 RPM
SRP007412_kidney	0.10 RPM	0.97 RPM
SRP007412_liver	0.00 RPM	3.83 RPM
SRP007412_testis	0.00 RPM	216.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_697 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_697 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1096
Gorilla gorilla	retro_ggor_862
Macaca mulatta	retro_mmul_850

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151725	1 retrocopy	retro_hsap_1096,
Gorilla gorilla	ENSGGOG00000011892	1 retrocopy	retro_ggor_862,
Microcebus murinus	ENSMICG00000013084	1 retrocopy	retro_mmur_836,
Macaca mulatta	ENSMMUG00000012176	1 retrocopy	retro_mmul_850,
Nomascus leucogenys	ENSNLEG00000010967	1 retrocopy	retro_nleu_1628,
Oryctolagus cuniculus	ENSOCUG00000003903	1 retrocopy	retro_ocun_1174,
Pongo abelii	ENSPPYG00000015238	1 retrocopy	retro_pabe_979,
Pan troglodytes	ENSPTRG00000016643	1 retrocopy	retro_ptro_697 ,