RetrogeneDB ID: retro_ggor_814

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:74758181..74759370(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTN4IP1
• Ensembl ID: ENSGGOG00000008254
• Aliases: None
• Description: None

Sequence

>retro_ggor_814
ATGGAATTTCTGAAGACTTGTGTACTTAGAAGAAATGCGTGTACTGTGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAAAG
GCCTTCCATTAGAAGGATTAGTACTACCTCTCCAAGGAGCACTGTCATGCCTGCTTGGGTGATAGATAAGTATGGGAAGA
ATGAAGTGCTTCGATTGACTCAGAACGTGATGATACCTATCAAACGCTGTCCAAATGAAGTCATTGTAAAAGTTCACCCT
GCCAGTGTAAATCCTATAGACGTCAATATGAGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCGTAATCCTTTACA
CATGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTGGTTCGGGATGTCTCTGGCATGGTGATGGAATGCGGGCTTGATG
TGAAGTACTTCAAGCCTTGAGATAAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTA
GTCAGTGGAAATGAGGTCTCTCACAAACCCAAATCACTCACTCATATATCAAGCTGCCTCTTCGCCATATGTGGCTCTCA
CAGCCTCATCTGCCGTAAACAAAGTTGGTGACCTGAATGACAAGAATTGCACAGAAAGACGTGTTCTAATCTTAGGCGCT
TCAGGCGGAGTTGGTAGTTTTGCTATATAGGTAATGAAAGCATGGGATGCTCATGTGACAGCAGTTTGCGCTCAAGATGC
CAGTGAGCTTATAAAGAAGCTTGGGGCAGATGATGTAATTGATTACAAATTTGGAAGTGTGGAAGAGCAGTTGAAATCCT
TAAAACCGTTTGACTTCATCCTTGGTAATGTTGGCAGATCCACTGAAACATGGGCTCCAGATTTTCTCAAGAAATGGTCA
GGAGCCACCTATGTGACTTTGGTGAGTCCTTTCCTCCTGAACATGGACTTATTGGGCATAGCAGATGGCATGTTGCAGGC
AGGAGTCACCATAGGTTTGAAGGCATTAAAGCATTTCTGGAAAGGAGTCCATTATCGCTGGGCGTTTTTCATGGCCAGTG
GTCCACGTTTAGGTGACATCGCAGAACTGGTGGATGTGGGAAAAATTGGGCCAGTTATTGAACAAACTTTCCCTTTTTCT
AAAGTTCCGGAAGCCTTCCTTAAGGTGGAAAGAGGACACACATGAGGAAAGACTGTAATTAATGTTGTT

Alignment

ORF - retro_ggor_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHY
          MEFLKTCVLRRNACT.VCFWRSKVVQ.PS.RRISTTSPRSTVMPAWVIDKYGKNEVLR.TQN.M.PI...
Retrocopy MEFLKTCVLRRNACTVVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNVMIPIKRC

Parental  PNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPG
          PNEVIVKVH.ASVNPIDVNMRSGYGATALNMKR.PLH.KIKGEEFPLTL.RDVSG.VMECGLDVKYFKP.
Retrocopy PNEVIVKVHPASVNPIDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLVRDVSGMVMECGLDVKYFKP*

Parental  DEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRVL
          D.VWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SA.NKVG.LNDKNCT..RVL
Retrocopy DKVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASSPYVALTASSAVNKVGDLNDKNCTERRVL

Parental  ILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGG
          ILGASGGVG.FAI.VMKAWDAHVTAVC.QDASEL..KLGADDVIDYK.GSVEEQLKSLKPFDFIL.NVG.
Retrocopy ILGASGGVGSFAI*VMKAWDAHVTAVCAQDASELIKKLGADDVIDYKFGSVEEQLKSLKPFDFILGNVGR

Parental  STETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGPC
          STETWAPDFLKKWSGATYVTLV.PFLLNMD.LGIADGMLQ.GVT.G.KALKHFWKGVHYRWAFFMASGP.
Retrocopy STETWAPDFLKKWSGATYVTLVSPFLLNMDLLGIADGMLQAGVTIGLKALKHFWKGVHYRWAFFMASGPR

Parental  LDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV
          L.DIAELVD.GKI.PVIEQTFPFSKVPEAFLKVERGH..GKTVINVV
Retrocopy LGDIAELVDVGKIGPVIEQTFPFSKVPEAFLKVERGHT*GKTVINVV

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	8.39 RPM
SRP007412_cerebellum	0.00 RPM	6.11 RPM
SRP007412_heart	0.00 RPM	5.03 RPM
SRP007412_kidney	0.04 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	3.46 RPM
SRP007412_testis	0.00 RPM	7.04 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_814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_814 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1030
Pan troglodytes	retro_ptro_705
Pongo abelii	retro_pabe_863

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130347	1 retrocopy	retro_hsap_1030,
Gorilla gorilla	ENSGGOG00000008254	1 retrocopy	retro_ggor_814 ,
Nomascus leucogenys	ENSNLEG00000013349	1 retrocopy	retro_nleu_908,
Otolemur garnettii	ENSOGAG00000012703	1 retrocopy	retro_ogar_590,
Pongo abelii	ENSPPYG00000016882	1 retrocopy	retro_pabe_863,
Pan troglodytes	ENSPTRG00000018461	1 retrocopy	retro_ptro_705,