RetrogeneDB ID: retro_ggor_2402

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:19066211..19067450(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSGGOG00000028420
• Aliases: None
• Description: None

Sequence

>retro_ggor_2402
TCTCCTACTTGAGAACTAGCCATGCAAACTTTTGGTGTTCTTACGGAGCTAAAGACTTGCCAGGTACATACCTATGGGTT
GATAATGGGTGACAGTAACAGATCTGCTGAAGCACAGAAACTTGCTAATGGGATCAACATCATTGTGGCCACACCAGGCT
GTCTGCTGGACCATATGCAGAATACCCCAGGGTTTATGTATAAAAACCTGCAGTGTCTGGTTATTGATGAAGCTGATCAT
ATCTTGGATGTTGGGTTTGAAGAGGAATTAAAGCAAGTTATTAAACTTTTGCCAACACGTAGACAGACTATGCTCTTTTC
TGCCACCCAAACTCGAAAAGTTGAAGGCCTGGCAAGGATTTCTCTGAAAAAGGAGCCATTGTATGTTGGTGTTGATGATG
ATAAAGCTAATGCAACAGTGAATGGTCTTGAGCAGGGATATGTTGTTTGTCCTTCCAAAAAGAGATTCCTTCTGCTCTTT
ACATTCCTTAAGAAGAAACAAAAGAAGAAGCTTATGGCCTTCTTTTCATCTTGTATGTCCGTGAAATACCCCTATGAGTT
GCTGAACTACGTTGATTTGCCCTACATGGCCATTCATGGAAAGCAAAAGCAAAATAAGTGTACAACCACATTCTTCCAGT
TCTGCAACCCAGATTCAGGAACACTATTGTGTACGGATGTGGCAACAAGAGGACTGGACATTCCTGAAGTTGACTGGATT
GTTCAGTATGACCCTCCGGATGACCCTAAGGAATATATTCATTGTGTGGGTAGAACAGCCAGAGGGCTAAATGGGAGAGG
GCATGCCCTGCTCATTTTGTGCCCAGAATAATTGGATTTTCTTCGCTACTTGAAACAATCCAAGGTTCCATTGAGTTTAT
TAGAATTTTTCTGGTCTAAAATTTCTGACATTAAGTCCCAGCTTGAGAAATTGATTGAAAAGAACTACTTTCTTCGTACG
TCAGCCCAGAAACCATATAAGCCATACATACAAGCCTATGATTCCCATTCTCTGAATCAGATCTTTAATGTTAATAACTT
AAATTTGCCTCAAGTTGCTCTTTCATTTGGTTTCAAGGTGACTCCCTTTGTTGATCTGAACATCAACTGCAATGAAGCCA
AGCAGAAAAAGCAAGGGGGTGGTGGTGGATTTGGCTACCAGAAAACCAAGAAAATTGAGAAGTCCAAAATCTTTAAATAC
ATTAGCAAGATATCATCCGACAGCAGGCAGTTCTCTCAC

Alignment

ORF - retro_ggor_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 61.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNL
          SPT.ELAMQTFGVL.EL.T..VHTYGLIMG.SNRSAEAQKLANGINIIVATPG.LLDHMQNTPGFMYKNL
Retrocopy SPT*ELAMQTFGVLTELKTCQVHTYGLIMGDSNRSAEAQKLANGINIIVATPGCLLDHMQNTPGFMYKNL

Parental  QCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATV
          QCLVIDEAD.ILDVGFEEELKQ.IKLLPTRRQTMLFSATQTRKVE.LARISLKKEPLYVGVDDDKANATV
Retrocopy QCLVIDEADHILDVGFEEELKQVIKLLPTRRQTMLFSATQTRKVEGLARISLKKEPLYVGVDDDKANATV

Parental  DGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTT
          .GLEQGYVVCPS.KRFLLLFTFLKK..KKKLM.FFSSCMSVKY.YELLNY.DLP..AIHGKQKQNK.TTT
Retrocopy NGLEQGYVVCPSKKRFLLLFTFLKKKQKKKLMAFFSSCMSVKYPYELLNYVDLPYMAIHGKQKQNKCTTT

Parental  FFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGF
          FFQFCN.DSGTLLCTDVA.RGLDIPEVDWIVQYDPPDDPKEYIH.VGRTARGLNGRGHALLIL.PE.L.F
Retrocopy FFQFCNPDSGTLLCTDVATRGLDIPEVDWIVQYDPPDDPKEYIHCVGRTARGLNGRGHALLILCPE*LDF

Parental  LRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLA
          LRYLKQSKVPLS...F.WSKISDI.SQLEKLIEKNYFL..SAQ..YK.YI.AYDSHSL.QIFNVNNLNL.
Retrocopy LRYLKQSKVPLSLLEFFWSKISDIKSQLEKLIEKNYFLRTSAQKPYKPYIQAYDSHSLNQIFNVNNLNLP

Parental  QVALSFGFKVPPFVDLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISRKSSDSRQFSH
          QVALSFGFKV.PFVDLN.N.NE.KQKK.GGGGGFGYQKTKK.EKSKIFK.IS..SSDSRQFSH
Retrocopy QVALSFGFKVTPFVDLNINCNEAKQKKQGGGGGFGYQKTKKIEKSKIFKYISKISSDSRQFSH

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	0.10 RPM	22.92 RPM
SRP007412_cerebellum	0.16 RPM	26.32 RPM
SRP007412_heart	0.00 RPM	4.88 RPM
SRP007412_kidney	0.04 RPM	34.92 RPM
SRP007412_liver	0.03 RPM	19.84 RPM
SRP007412_testis	0.21 RPM	43.82 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_2402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2402 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3561
Pan troglodytes	retro_ptro_2419

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Echinops telfairi	ENSETEG00000017166	2 retrocopies	retro_etel_1919, retro_etel_297,
Homo sapiens	ENSG00000088205	6 retrocopies	retro_hsap_1361, retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402 , retro_ggor_535,
Microcebus murinus	ENSMICG00000017590	1 retrocopy	retro_mmur_1560,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865,
Nomascus leucogenys	ENSNLEG00000011769	4 retrocopies	retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Pongo abelii	ENSPPYG00000012796	4 retrocopies	retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes	ENSPTRG00000012391	5 retrocopies	retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,