RetrogeneDB ID: retro_ggor_1461

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:54735146..54736454(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD3
• Ensembl ID: ENSGGOG00000001793
• Aliases: None
• Description: None

Sequence

>retro_ggor_1461
ATGGCGGCTGTAGCTGCTGTTCGCTGGCTGGGGCTCTGCAGCAGGCTTGACCAGCCACTGACGGGTCAGCCAGCAGGTCT
GTGTGAACAGGCACACAGCTGAGATTTTATTCTGGAAGTGCAACCCTCTCAAATATTGAAGGAACTGATATAACAGGGAT
TGAAGAAGTAGTAATTCCAAAAAAGAAAACTTGGGATAAAGTAGCCGTTCTTCAGGCTCTTGCATCCACAGTAAACAGGG
TTCCCACGGCTGTACCTTGCGTGTTTCAAGATAATCCTTACATCATACCAACATCCTCTTCAGAATCTCGTTCATTTTTA
CTGGCAAAGAAATCCGGGGAGAATACGGCCAAGTTCATTATTAATTCATACTCCAAATATTTTCAGAAAGACATAGCTGA
ACCTCATACACTGTGTTTAATGCCTGAGTACTTTGAACCTCAGATCAAAGACGTGAGTGAAGCCACTCTCAAGGAACGAA
TCAAGCTCAGAAAAGTCAAAGTCTCTGTGGACATGTTTGATGAGCTTTTGCAAGCAGGAACCACGGTGTCTCTTGTAACA
ACATATAGTCTCTTGGATTTATTGTGTTACTATGGTGACCAGGAGCCCTCAACTGATTATCAGTTTCAACAAATTGAACA
GTCAGAAGAATTGGAAGAGGAAAATAATAAGGGGTCTAGGAGGAAAGCTGGTCATCAGTTTGGAGTTACCTGGTGAGCAC
AAAACAACGCTGAGAGAATGTTTTCTCTAATGCCAGAGAAAAATGCACATTCCTATTGCACAGTGATCCGAGGAATGGTG
AAGCACCAAGCTTATGAGCAGGCATTAAACCTGTACACTGAGTTACTAAACAACAGACTCTGTGCTGATGTATACACATT
TAATGCAGTGATTGAAGCAACAGTATTGGTGATAAATGAGAAATTTGAGGAAGAATGGAATAATATACTGGAGCTGCTAA
GACAAATGGTTGCACAGAAGGTGAAACCAAATCTACAGACTTTTAATACCATTCTGAAATGTCTCCGAAGATTTTATGTA
CTTGCAAGATTGCCAGCCTTACAGATTCTACGTGAAATGAAAGCCATCAGACTAGAACCCTCGCTTGCAACATATCACCA
TATTATTCAGCTGTTTATCAGCCTGGAAACCCTTCAAAGGGATCATCTTTCATCATCTATGATATAATGAATGAATTAAT
GGGAAAGAGATTTTCCCCCAAAGGACCTGGATGATGATGTTTTTTCAGTCAGCCATGAGAGTATCTTCGTCTCTCAGAAA
TCTAGAACTTGCGTACCAAATACATGGC

Alignment

ORF - retro_ggor_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 63.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAVSAVRWLGLRSRFGQPLTGRRAGLCEQARS-CRFYSGSATLSKVEGTDITVGIEEVVIPKKKTWDKV
          MAAV.AVRWLGL.SR..QPLTG..AGLCEQA.S..RFYSGSATLS..EGTDIT.GIEEVVIPKKKTWDKV
Retrocopy MAAVAAVRWLGLCSRLDQPLTGQPAGLCEQAHS<LRFYSGSATLSNIEGTDIT-GIEEVVIPKKKTWDKV

Parental  AVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFIINSYPKYFQKDIAEPHIP
          AVLQALASTVNR..TAVP.VFQD.PY..P.SS.ESRSFLLAKKSGEN.AKFIINSY.KYFQKDIAEPH..
Retrocopy AVLQALASTVNRVPTAVPCVFQDNPYIIPTSSSESRSFLLAKKSGENTAKFIINSYSKYFQKDIAEPHTL

Parental  CLMPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYYGDQEPSTDYH
          CLMPEYFEPQIKD.SEA.LKERI.LRKVK.SVDMFD.LLQAGTTVSL.TT.SLLDLLCYYGDQEPSTDY.
Retrocopy CLMPEYFEPQIKDVSEATLKERIKLRKVKVSVDMFDELLQAGTTVSLVTTYSLLDLLCYYGDQEPSTDYQ

Parental  FQQTGQSGALEEENDETSRRKAGHQFGVTWRAKNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNL
          FQQ..QS..LEEEN...SRRKAGHQFGVTW.A.NNAER.FSLMPEKN.HSYCT.IRGMVKH.AYEQALNL
Retrocopy FQQIEQSEELEEENNKGSRRKAGHQFGVTW*AQNNAERMFSLMPEKNAHSYCTVIRGMVKHQAYEQALNL

Parental  YTELLNNRLHADVYTFNALVEATVCAINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVF
          YTELLNNRL.ADVYTFNA..EATV..INEKFEE.W..ILELLR.MVAQKVKPNLQTFNTILKCLRRF.V.
Retrocopy YTELLNNRLCADVYTFNAVIEATVLVINEKFEEEWNNILELLRQMVAQKVKPNLQTFNTILKCLRRFYVL

Parental  ARSPALQVLREMKAIGIEPSLATYHHIIHLFD-QPGDPLKRSSFIIYDIMNELMGKRFSP-KDLDDDK-F
          AR.PALQ.LREMKAI..EPSLATYHHII.LF..QPG.P.K.SSFIIYDIMNELMGKRFSP.KDL.DD..F
Retrocopy ARLPALQILREMKAIRLEPSLATYHHIIQLFI<QPGNPSKGSSFIIYDIMNELMGKRFSP>KDL-DDD>F

Parental  FQSAMSICSSLRDLELAYQVHG
          FQSAM...SSLR.LELAYQ.HG
Retrocopy FQSAMRVSSSLRNLELAYQIHG

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	46.23 RPM
SRP007412_cerebellum	0.59 RPM	53.31 RPM
SRP007412_heart	0.06 RPM	17.35 RPM
SRP007412_kidney	0.08 RPM	66.53 RPM
SRP007412_liver	0.11 RPM	55.37 RPM
SRP007412_testis	0.21 RPM	132.09 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_1461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1461 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2017
Pongo abelii	retro_pabe_1653

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132300	1 retrocopy	retro_hsap_2017,
Gorilla gorilla	ENSGGOG00000001793	1 retrocopy	retro_ggor_1461 ,
Nomascus leucogenys	ENSNLEG00000002493	1 retrocopy	retro_nleu_2729,
Pongo abelii	ENSPPYG00000012216	1 retrocopy	retro_pabe_1653,