RetrogeneDB ID: retro_ggor_2264

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:59531387..59532551(-)
• Located in intron of: ENSGGOG00000001874

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGGOG00000004480
• Aliases: None
• Description: None

Sequence

>retro_ggor_2264
ATGAGGTGGGTGGCCCTGTTCCTGAACGGCAGCCCCAAGAACGGAAAGGTGGTTGCTGTATGTGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGTGGTAAACTTGGCATAAAGGCCACCAGTGTGTATAATGGCAAAGGTGGACTGATTGATGATATTG
CTTCGGTCAGGGATGATGATGTTTTGTTTGTGTGTGAAGGAGAGCCGTTTATTGATCCTGACAGATTCTAAACCACCTGA
GGGATTGTCAGGATTCTACATAGACTGGCTAACATTAAATGCTGGAGGGCGGTACTTTACAACCACACAGAGCACTTTAG
TGAATAAAGAACCTGATAGTATGCTGGCCCACATGTTTAAGGACAAAGATGTCTGGGAAATAAGCAAGATCACAGAGGAG
TTTTCTTAATTGACCGAAGTCCTGAGTACTTTGAACCCATTTTGAACTACTTGCGTCATGGACAGCTTATTGTACATGAT
GGCATTAATTTATTGGATATGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAGAAATGGCAAT
AAAGGATTCTAAACCACCGGAGGATCATTCACCAATATCCTGAAAGGAATTTGTCTTAATTTTGGTGGCAACTTCAATCA
AGTCAGAAGTGCAATGCCAAGGTTTGAACTTCAGTGGTGCTGATCTTTCTCATTTGGACCTTTGAAACATTAACTTCAAA
ATGGCCAGTTTAAGCCGCTGCAGTCTTGCACATGCAAATCTTTGCTGTGCAAATCTTAAACAAGCTGATCTCTCTGGATC
AGTGCTTGACTGTGCAAATCTCCAGGGAGTCAAGACACTCTGTTCTAATGTAGAAGGAGCATCCCTGAAACTGTGTAATT
TTGAGGATCCTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAACCTGAAAGGTGTGGATATGGAAGGAAGTCAGATAACA
GGAATTAACCTGAGAGTGACTACCTTAAAAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTGGCAGGAAC
TGATTTAGAGAATTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACCTGAGAGGGTCCAACATGAAGGGAGCTAGAC
TTGAAGAGATGCTAACACCACTACACATGTCACAAAGTGTTAGA

Alignment

ORF - retro_ggor_2264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDD-VLFVCEGE
          MR.V.LFLNGSPKNGKVV.AV.GTLSDLLSVAS.KLGIKATSVYNGKGGLIDDIA..R.DD.....C..E
Retrocopy MRWVALFLNGSPKNGKVV-AVCGTLSDLLSVASGKLGIKATSVYNGKGGLIDDIASVR-DD>MFCLCVKE

Parental  PFIDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRILRSTLVNKEPDSMLAHMFKDKGVW-GNKQDHRG
          ......TDSKPPEGL.GF..DWLTLN.GGRYFTTT....STLVNKEPDSMLAHMFKDK.VW.GNKQDHRG
Retrocopy SRLLILTDSKPPEGLSGFYIDWLTLNAGGRYFTTTQ---STLVNKEPDSMLAHMFKDKDVW<GNKQDHRG

Parental  AFLIDRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKE
          .FLIDRSPEYFEPILNYLRHGQLIV.DGINLL..LEEARFFGIDSLIEHLE.AIK.S.PPEDHSPIS.KE
Retrocopy VFLIDRSPEYFEPILNYLRHGQLIVHDGINLLDMLEEARFFGIDSLIEHLEMAIKDSKPPEDHSPIS*KE

Parental  FVRFLLATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCAN
          FV..L.AT..KSE..CQGLNFSGADLS.LDL..INFKMA.LSRC.LAHANLCCANL..ADLSGSVLDCAN
Retrocopy FVLILVATSIKSEVQCQGLNFSGADLSHLDL*NINFKMASLSRCSLAHANLCCANLKQADLSGSVLDCAN

Parental  LQGVKMLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKN-KLKNCNLRGAT
          LQGVK.LCSN.EGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQ.TGINLRV.TLKN.KLKNCNLRGAT
Retrocopy LQGVKTLCSNVEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQITGINLRVTTLKNAKLKNCNLRGAT

Parental  LAGTDLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          LAGTDLENCDLSGCDLQEANLRGSN.KGA..EEMLTPLHMSQSVR
Retrocopy LAGTDLENCDLSGCDLQEANLRGSNMKGARLEEMLTPLHMSQSVR

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	0.19 RPM	7.86 RPM
SRP007412_cerebellum	0.24 RPM	7.60 RPM
SRP007412_heart	0.13 RPM	11.32 RPM
SRP007412_kidney	0.12 RPM	9.32 RPM
SRP007412_liver	0.08 RPM	5.51 RPM
SRP007412_testis	0.10 RPM	18.13 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_2264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2264 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1218

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264 , retro_ggor_2791,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,