RetrogeneDB ID: retro_ptro_933

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:68256692..68258297(+)
• Located in intron of: ENSPTRG00000006478

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSPTRG00000012391
• Aliases: None
• Description: None

Sequence

>retro_ptro_933
GGGGAATCTGAAGAAGAAAGTGCCAAGTCTCCTAAAGAAACAGAAAATAATGTTGAGAAGCCAGATGATGAAGATGACAG
TGAGGTGCCCAGCCTGCCCCTGGGACTGACAGGAGCTTTTGAGGATACTTCATTTGCTTCTTATGTAATCTTGTCAATGA
AAACACTCTGAAGGCAATAAAAGAAATGGGTTTTACAAACGTGACTGAAATTCAGCATAAAAGTATCAGACCACCTCTGG
AAGGCAGGGATCTTCTTGCAGCTACAAAAACCGTCAGTGGTAAAACCCCAGCTTTTCTCATCCTGCAGCTGAACTCATTG
TTAAGTTAAATTTCATGCCCAGGAATGGAACAGGGGTCCTTATTCTCTCACCTACTAGAGAACTAGACATGCAAACTTTT
GGTGTTCTTAAGGAGCTAATGAGTCACCACGTGCATACCTATGGGTTGATAATGGGTGGCAGTAATAGATCTGCTGAAGC
ACAGAAACTTGCTAATGGGATCAACATCACTGTGGTCACACCAGGCTGTCTGCTGGACCATATGCAGAATATCCCAGGGT
TTATGTATAAAAATCTGCAGTGTCTGGTTATCGATGAAGCTGATCGTATCTTGGATGTTGAGTTTGAAGAGGAATTAAAA
CAAATTATTAAACTTTTGCCAACACGTAGACAGACGATGCTCTTTTCTGCCACCCAAACTTGAAAAGTTGAAGGCCCGGC
AAGGACTTCTCTGAAAAAGGAGCCATTGTATGTTGGTGTTGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAGC
AGGGATATGTTGTTTGTCCTTCTGAAAAGAGATTCCTTCTACTCTTTACATTCCTTAAGAAGAACCAAAAAAAGAAGCTT
ATGGCCTTCTTTTCATCTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCATCTTGGCCAT
TCATGGAAAGCAAAAGCAAAATAAGCATACGACCACATTCTTCCAGTTCTGCAATGCAGATTCAGGAACACTATTGTGTA
CAGATGTGGCAGCAAGAGAACTGGACATTACTGAAGTCAACTGGATTGTTCAGTATGACCCTCCGGATGACCCTAAGGAA
TAATATTCATCGTGTGGGTAGAACAGCCAGAGACCTAAATGGGAGAGGGCATGCCTTGCTCATTTTGCACCCAGAAGAAT
TGGGTTTTCTTCACTACTTGAAATGATCCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATT
CAGTCTCAGCTTGAGAAATTGATTCAAAAGAACTACTTTTTTCATAAGTCAGCTCAGGAAGCATATAAATCATACATACA
AACCTACGATTCCCATTCTCTGAAACAGATCTTTAATGTTTAATAACTTAAATTTGCCTCAAGTTGCTGTCATTGGTTTC
AAGGTGCCTCCCTTTGTTGATCTGAACGTCAACAGCAATGAAGGCAAGCAGAAAAAGCGAGTAGGCAGTGGTGGATTTGG
CTACCAGAAAACCAAGAAAGTTGAGAAGTCCAAAATCTTTAAACATATTAGCAAGCAAACATCCAATCGCAGGCAGTTCT
CTCAC

Alignment

ORF - retro_ptro_933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.02 %
• Parental protein coverage: 80.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKSEEESAETPKETENNVDKPDNDEDESEVPNLPLGLTGAFEDTSFAS-LCNLVNENTLKAIKEMGFTNM
          G.SEEESA..PKETENNV.KPD.DED.SEVP.LPLGLTGAFEDTSFAS.LCNLVNENTLKAIKEMGFTN.
Retrocopy GESEEESAKSPKETENNVEKPD-DEDDSEVPSLPLGLTGAFEDTSFAS<LCNLVNENTLKAIKEMGFTNV

Parental  TEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLI-PAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVL
          TEIQHKSIRP.LEGRDLLAA.KT.SGKT.AFLI.PA.ELIVKL.FMPRNGTGVLILSPTREL.MQTFGVL
Retrocopy TEIQHKSIRPPLEGRDLLAATKTVSGKTPAFLI<PAAELIVKLNFMPRNGTGVLILSPTRELDMQTFGVL

Parental  KELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDV
          KELM.HHVHTYGLIMGGSNRSAEAQKLANGINI.V.TPG.LLDHMQN.PGFMYKNLQCLVIDEADRILDV
Retrocopy KELMSHHVHTYGLIMGGSNRSAEAQKLANGINITVVTPGCLLDHMQNIPGFMYKNLQCLVIDEADRILDV

Parental  GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEK
          .FEEELKQIIKLLPTRRQTMLFSATQT.KVE..AR.SLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEK
Retrocopy EFEEELKQIIKLLPTRRQTMLFSATQT*KVEGPARTSLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEK

Parental  RFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLC
          RFLLLFTFLKKN.KKKLM.FFSSCMSVKYHYELLNYIDLP.LAIHGKQKQNK.TTTFFQFCNADSGTLLC
Retrocopy RFLLLFTFLKKNQKKKLMAFFSSCMSVKYHYELLNYIDLPILAIHGKQKQNKHTTTFFQFCNADSGTLLC

Parental  TDVAARGLDIPEVDWIVQYDPPDDPKE-YIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSE
          TDVAAR.LDI.EV.WIVQYDPPDDPKE..IHRVGRTAR.LNGRGHALLIL.PEELGFL.YLK.SKVPLSE
Retrocopy TDVAARELDITEVNWIVQYDPPDDPKE>NIHRVGRTARDLNGRGHALLILHPEELGFLHYLK*SKVPLSE

Parental  FDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNV-NNLNLPQVALSFGFKVPP
          FDFSWSKISDIQSQLEKLI.KNYF.HKSAQEAYKSYI..YDSHSLKQIFNV.NNLNLPQVA...GFKVPP
Retrocopy FDFSWSKISDIQSQLEKLIQKNYFFHKSAQEAYKSYIQTYDSHSLKQIFNV>NNLNLPQVAV-IGFKVPP

Parental  FVDLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISKKSSDSRQFSH
          FVDLNVNSNEGKQKKR.G.GGFGYQKTKKVEKSKIFKHISK..S..RQFSH
Retrocopy FVDLNVNSNEGKQKKRVGSGGFGYQKTKKVEKSKIFKHISKQTSNRRQFSH

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	0.05 RPM	18.52 RPM
SRP007412_cerebellum	0.14 RPM	42.48 RPM
SRP007412_heart	0.06 RPM	23.87 RPM
SRP007412_kidney	0.21 RPM	31.98 RPM
SRP007412_liver	0.03 RPM	26.09 RPM
SRP007412_testis	0.00 RPM	36.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_933 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_933 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1361
Pongo abelii	retro_pabe_1128
Macaca mulatta	retro_mmul_2192

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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 ,