RetrogeneDB ID: retro_ggor_1366

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:8483777..8485020(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFWD2
• Ensembl ID: ENSGGOG00000013437
• Aliases: None
• Description: None

Sequence

>retro_ggor_1366
AGCCTAGGCAGCAGCAGGAGGCAACCTCTGCTTGCCCCTCCCCTCTCCAACAGGCTCATCAATTCATATAAGGACAACAG
CAATGATTTCATATGCCCCATCTGCTTTGATATGATTGAAGAGGCATACACGACAAAATAAGGCCACAGCTTTTGCTATA
AGTAGATTCACTAGAGTTCGGAGGACAATAATATATGTACCAAGTATAACTATGTTGTGGACAATACTAACCATCTGTTT
CCTAATTTGTTGGTGAATGAGCTCATTCTCAAACAGAAGCAAAGATTTGAGGAAAAGAGGTTCAAATTGGACCACTCAGT
GAGTAGCACCAATGGCCACAGGTGGCGAATATTTCAAGATTTGTTGGGAACTGACCAAGATAACCTTGATTTGGCCAATA
TCAACCTCATGTTGGAGTTACTAGTTCAGAAGAAGAAACAACTGGAAGCAGAATCACACGCAGCCTAACTACAGAATCTT
ATACAATTCCTCAAGGTTGCAAGAAGAAATAGGAGAGAGCAACTGGGACAGTTCCAGAAGGAGCTAAGTGTTTTGGAAGA
GGATATTAAAAGAGTGGAAGAAATGAGTGGCTTACACTCTCCTGTCAGTGAGGATAGGACAGTGCCTCAACTTGAAGCTC
CTTCTGCATCACACAGTAGCATTATGGATTCCACAGAATATAGCCAACATCCAGGTTTCAGTGGCAGTTCTTAGACAAAG
AAACAGCCTTGATATAACAGCACATTAACATCAAAATTAAAATGGCCCACTGCTCATTTTGAAGACCTGGAGCACTGTTA
CTTTTCTACAAGGTTGTCTCGTATCTCAGATGACAGTTGAACGCAAGCCAATTGGATGAACTTCAGAAATGCTTGTCCAA
GGTTACTCAATATAAATCAATATGAACTTTAGCCACATTATCATGCCCTAGTGGTCTCTATAATGATTCCAGGATAGTAT
CTGGTATTGAATTTGACCAGGATTGTGACTATTTTGCAATTGCTGAGGTTACAATGAAGATTAAAGTCTATGAATATGGC
ACAGTCATCCAGGATGCAGTGGATATTCATTACCGTGTGAATGAAATGACCTCAATTCCAAAATCAGCTGTATCAGTTGG
AGTAGTTACCATAAGAACCTGTTAGCTAGCAGTGATTATGAAGGCATTGCTATCCTATGGGATGGATTCACAGGACAGAG
GTCAAAGGTGTAACAGGAGCATGAGAAGAGGTGTTGAAGTGTT

Alignment

ORF - retro_ggor_1366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 75.77 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVSGSRKRPLLAP-LCNGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCN
          ....SR..PLLAP.L.N.LINSY.D.SNDF.CPICFDMIEEAY.TK.GHSFCYK.IH.S.EDNN.C.K.N
Retrocopy SLGSSRRQPLLAPPLSNRLINSYKDNSNDFICPICFDMIEEAYTTK*GHSFCYK*IH*SSEDNNICTKYN

Parental  YVVDNVDHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNLMLEL
          YVVDN..HL.PN.LVNELILKQKQRFEEKRFKLDHSVSSTNGHRW.IFQD.LGTDQDNLDLAN.NLMLEL
Retrocopy YVVDNTNHLFPNLLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWRIFQDLLGTDQDNLDLANINLMLEL

Parental  LVQKKKQLEAESHAAQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQ
          LVQKKKQLEAESHAA.LQ.L..FLKVARRN.REQL.Q.QKELSVLEEDIKRVEEMSGL.SPVSED.TVPQ
Retrocopy LVQKKKQLEAESHAA*LQNLIQFLKVARRNRREQLGQFQKELSVLEEDIKRVEEMSGLHSPVSEDRTVPQ

Parental  FEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISGIDD
          .EAPS.SHSSI.DSTEYSQ.PGFSGSS.TKKQP.YNSTL.S..K..TAHFEDLE.CYFSTR.SRIS..DD
Retrocopy LEAPSASHSSIMDSTEYSQHPGFSGSS*TKKQP*YNSTLTSKLKWPTAHFEDLEHCYFSTRLSRIS--DD

Parental  SRT-ASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYD
          S.T.ASQLDE.Q.CLSK.T.Y.S...LATLS..S.LYN.S.IVS.IEFD.DCDYFAIA.VT.KIKVYEY.
Retrocopy S*T<ASQLDELQKCLSKVTQYKSI*TLATLSCPSGLYNDSRIVSGIEFDQDCDYFAIAEVTMKIKVYEYG

Parental  TVIQDAVDIHYPENEMT-CNSKISCISWSSYHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSV
          TVIQDAVDIHY..NEMT..NSKISCISWSSYHKNLLASSDYEG..ILWDGFTGQRSKV.QEHEKRC.SV
Retrocopy TVIQDAVDIHYRVNEMT<LNSKISCISWSSYHKNLLASSDYEGIAILWDGFTGQRSKV*QEHEKRC*SV

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	10.84 RPM
SRP007412_cerebellum	0.00 RPM	9.18 RPM
SRP007412_heart	0.00 RPM	1.91 RPM
SRP007412_kidney	0.00 RPM	11.78 RPM
SRP007412_liver	0.03 RPM	12.90 RPM
SRP007412_testis	0.10 RPM	27.56 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_1366 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1366 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1281
Macaca mulatta	retro_mmul_1342

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000011313	4 retrocopies	retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366 ,
Macaca mulatta	ENSMMUG00000002072	1 retrocopy	retro_mmul_1342,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678,
Nomascus leucogenys	ENSNLEG00000015420	1 retrocopy	retro_nleu_1225,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281,