RetrogeneDB ID: retro_ggor_862

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:25446706..25447920(-)
• Located in intron of: ENSGGOG00000003082

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSGGOG00000011892
• Aliases: None
• Description: None

Sequence

>retro_ggor_862
CAGCCTCCCGGGCATGCAGGTCCATGATATTCAAAGAATATTTTATGAAGAATACATCCTGTGAAAGATAAAGCTGGTCA
AAAGTGCAAGCCTACCAATGTGTTTGATTTTCCTAATAATTCTGCTGTCTCAAGAATTGGCAGGCTTGGTGAAAATGAGA
AAGATGAAGAACATTATGAAACCTTTGATCCTCCTTTACACAGCTCATCTATGTATGCCAATGAAGAATTCTCCAAATAT
TGTGGATTATCTATCACTTCAACTCCTGCAGGAAAAGAAGCAAAAAGAAGCTCGAGCACTTCTGAAAATGAAGGAAGTGA
AAACGAATCTGCAAAAATGAGTGCAAAAAGCCAGGAAGAAAACTCAAACTCAGCGAGGAGTCTGAAAGCACTGAAGAAAG
TGATGTGAGAAGAAAAGTTAAGTCAGTGGAGAAAATAAAGACCCAACAACATGAGGCTATTCCAACTACAGCATCTTCAG
CCCTTTCAGAGAAACCAGCCAACTCAGTCACTTCCAAAACCATAGGACCCATTAATGCCCAGCCATCTGTTGAAAAAGAC
ACACTGACAACAGAAGGTCAAGCAAAACCCAGAAAAAAGGGAATACATCTTATGGCAAAAGGAAGAAATCAAGAAGTGAA
GCAATAGACTCAGATATTTCCAACATTGTGCATATTTGGTGTCTGGAAGGAAAGAAAACCAACGACATCATGGAATTGAA
TATTGTTTTGCCTGCATTTGAGAAAAACCTCGTCCAGTATAAACATAGAATAGAATCTAAAATTTGTAAGAAACACATCA
ATAAATTTTATTTTACTAGTAAAGAAGAACTCAACAAAATGCTTAAAAAGTCCAGATATTGAAAAATCTGAAAAAGAAGA
ATGCTAAGGTAATTTCAGATATCAAAAAGAAATGACAGTGTTTGACGGAAGTCCAGGATGAGCTGCTTTGGTTAGAGCCA
CCAACTGAAACAACTACAAACAAAATATTATGAACTTAAGGAGAGAACAGTCTTCCCTTAGGAATGCAGCTATTTCTTAT
CTAATTCAAAACAACTCCATCGGAAGTATTCAGATGTTCAGGAGAAAGAACCAAACGTAAAGGAAACATAAGATTCATCC
AGCCTTCCAGGTGTTATTTAAAGTAGGAACACTTTTGGGAGCTGAAAATCTTCTGTAAAATATCAGCCATCAATGAGAGA
AGCTCCTCCACCAG

Alignment

ORF - retro_ggor_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.71 %
• Parental protein coverage: 96.91 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RPHRSEGARCSKNTLERTHSMKDKAGQKCKPVDVFDFPDNSDVSSIGRLGENEKDEETYETFDPPLHSTA
          .P....G...SKN.L.R.H..KDKAGQKCKP..VFDFP.NS.VS.IGRLGENEKDEE.YETFDPPLHS..
Retrocopy QPPGHAGP*YSKNIL*RIHPVKDKAGQKCKPTNVFDFPNNSAVSRIGRLGENEKDEEHYETFDPPLHSSS

Parental  IYADEEEFSKHCGLSISSTPPGKEAKKSSDTSGNEASEIESVKISAK-KPGRKLRPISDDSESTEESDTR
          .YA.EE.FSK.CGLSI.STP.GKEAK.SS.TS.NE.SE.ES.K.SAK.KPGRKL...S..SESTEESD.R
Retrocopy MYANEE-FSKYCGLSITSTPAGKEAKRSSSTSENEGSENESAKMSAK<KPGRKLK-LSEESESTEESDVR

Parental  RKVKSAEKISTQRHEVIRTTASSELSEKPAESVTSKKTGPLSAKPSVEKENLSIESQ-SKTQKKGKMSHD
          RKVKS.EKI.TQ.HE.I.TTASS.LSEKPA.SVTSK..GP..A.PSVEK..L..E.Q.SKTQKKG..S..
Retrocopy RKVKSVEKIKTQQHEAIPTTASSALSEKPANSVTSKTIGPINAQPSVEKDTLTTEGQ<SKTQKKGNTSYG

Parental  KRKKSRSKAVGSDTSDIVHIWCPEGMKTSDIKELNIVLPEFEKTHLEHQQRIESKVCKAAIATFYVNVKE
          KRKKSRS.A..SD.S.IVHIWC.EG.KT.DI.ELNIVLP.FEK.......RIESK.CK..I..FY...KE
Retrocopy KRKKSRSEAIDSDISNIVHIWCLEGKKTNDIMELNIVLPAFEKNLVQYKHRIESKICKKHINKFYFTSKE

Parental  QFIKMLEES-QMLTNLKRKNAKMISDIEKKRQRMIEVQDELLRLEP-QLKQLQTKYDELKER-KSSLRNA
          ...KML..S.Q.L.NLK.KNAK.ISDI.KK.Q...EVQDELL.LEP.QLKQLQTKY.ELKER..SSLRNA
Retrocopy ELNKMLKKS<QILKNLKKKNAKVISDIKKK*QCLTEVQDELLWLEP>QLKQLQTKYYELKER>QSSLRNA

Parental  A-YFLSNLKQLYQDYSDVQAQEPNIKETYDSSSLPALLFKARTLLGA-ESHLRNINHQLEKLLDQ
          A.YFLSN.KQL...YSDVQ..EPN.KET.DSSSLP......R...G..E..L.NI.HQ.EKLL.Q
Retrocopy A<YFLSNSKQLHRKYSDVQEKEPNVKET*DSSSLPGVI-*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	0.05 RPM	0.38 RPM
SRP007412_cerebellum	0.08 RPM	0.24 RPM
SRP007412_heart	0.00 RPM	0.13 RPM
SRP007412_kidney	0.20 RPM	0.65 RPM
SRP007412_liver	0.08 RPM	28.20 RPM
SRP007412_testis	0.41 RPM	180.89 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_862 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1096
Pan troglodytes	retro_ptro_697
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,