RetrogeneDB ID: retro_ptro_448

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:90590046..90591693(+)
• Located in intron of: None

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_448
GTGAATGACGCTGGGCCTGATACAAAAAAAGCAAAAACTGAAAACAAAGGAGAATCTGAAGAATAAAGTGCCGAGACTTC
TAAAGAAACAGAAAATAATGTGGAGAAGCTAGATAATGATGAAGATGACAGTGAGGTGCCCAGCCTGCTCCTGGGACTGC
CAGGAGCTTTTGAGGATACTTCATTTGCTTCTCTATGTAATCTTGTCAATGAAAACACTCTGAAGGAAATAAAAGAAATG
GGCTTTACCAACATGGCTGAAATTCAGCATAAAACTATCAGACCACTTCTGGAAGGCAGGGATCTTCTAGCAGCTGTGAA
AACAGGCAGTGGTAAAACCTTGGCTGTTCTCATCCCTGCAATTGAACTCGTTGTTAAGTTAAAGTTCACGCCCAGGAATG
GAACAGGGGTCCTTATTCTCTCACCTACTAGACAACTAGCCATGCAAACTTTTGGTGTTCTTAAAGAGCTAATGACTCAC
CATGTGCACACCTATGGGTTGATAATAGGTAGCAGTAACAGATCTGCTGAAGCACAGAAACTTGCTAATGGGATCAACAT
CATTGTGGTCACACCAGGCCGTCTGCTGGACCATACGCAGAATACCCCAGGGTTTATGTATAAAAACCTGCAGGGTCTGG
CTATTGATGAAGCTGATTGTATCTTGGACGTTGGGTTTGAAGATAAATTAAAGCAAATTATTAAACTTTTGCCAACACGC
AGGCAGACTATGCTCTTTTCTGCCGCCTAAACTCGAAAAGTTGAGGACCTGGCAAGGATCTCTCCGAAAAAGGAGCCATT
GTATGTTGGTGTTGATGAAGATAAAGCTAATGCAACTGTGGATGGTCTTGAGCAGGGATACTTTGTTTGTCCCTCTGAAA
AGAGATACCTTCTGCTCTTACATTCCTTAAGAAGAACTGAAAGAAGAAGCTCATGGTCTTCTTTTCAGCTTGTATGTCTG
TGAAATACCCCTACGGGTTGCTGAAGTACATTGATTTGCTGTCTTGGCCATTCATGGAAAGCAAAAGCAAAATAAGCATA
CAACCACATTCTTCTAGTTCTGCAACGCAGATTCAGGAACACTATTGTGTAAGGATGTGGCAGCAAGAGGACTGGACATT
CCTGAAGTCAACTGGATTGTTCAGTATGACCCTCCAGATGACCCTAAGGAATGTATTCATTGTGTGAGGAGAACAGCCAG
AGGCCTAAATGGGGGAAGGCATGCCTTGCTCATTTTGCACCCAGAAGAACTGGGTTTCCTTCACTACTTGAAACAATCCA
AGGTTCCATTAAGTGAATTTGACTTTTCCTGATCTAAAATTTCTGACATTCAGTCTCAGCTTGAGAAACTGATTGAAAAG
AACTACTTTCTTCATAAGTCAGCCCAGGAAGCATATAAGTCATACATACAAGCCTATGATTCCTATTCTCTGAAACAGAT
CTTTAACATTAATAACTTAAATTTGCCTCACATTGCTCTGTCATTTGGCTTCAAGTTGCCTCCCTTTGTTGATCTGAACA
TGAACAGCAATGAAGGCAAGCAGAAAAAGCAAGGAGGATTTGGCTACCAGAAAACCAAGAAAGTTGAGAAGTCCATAATC
TTTAAACACATTAGCAAAAAGTCATCTGCAGCAGGCAGTTCCCTCAC

Alignment

ORF - retro_ptro_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 82.54 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VNDAEPDTKKAKTENKGKSEEESAETPKETENNVDKPDNDEDESEVPNLPLGLTGAFEDTSFASLCNLVN
          VNDA.PD.........G.SEE.SAET.KETENNV.K.DNDED.SEVP.L.LGL.GAFEDTSFASLCNLVN
Retrocopy VNDAGPDXXXXXXXXXGESEE*SAETSKETENNVEKLDNDEDDSEVPSLLLGLPGAFEDTSFASLCNLVN

Parental  ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLIL
          ENTLK.IKEMGFTNM.EIQHK.IRPLLEGRDLLAA.KTGSGKTLA.LIPA.EL.VKL.F.PRNGTGVLIL
Retrocopy ENTLKEIKEMGFTNMAEIQHKTIRPLLEGRDLLAAVKTGSGKTLAVLIPAIELVVKLKFTPRNGTGVLIL

Parental  SPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVATPGRLLDHMQNTPGFMYKNL
          SPTR.LAMQTFGVLKELMTHHVHTYGLI.G.SNRSAEAQKLANGINIIV.TPGRLLDH.QNTPGFMYKNL
Retrocopy SPTRQLAMQTFGVLKELMTHHVHTYGLIIGSSNRSAEAQKLANGINIIVVTPGRLLDHTQNTPGFMYKNL

Parental  QCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATV
          Q.L.IDEAD.ILDVGFE..LKQIIKLLPTRRQTMLFSA..TRKVEDLARIS.KKEPLYVGVD.DKANATV
Retrocopy QGLAIDEADCILDVGFEDKLKQIIKLLPTRRQTMLFSAA*TRKVEDLARISPKKEPLYVGVDEDKANATV

Parental  DGLEQGYVVCPSEKRFLLL-FTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDL-PVLAIHGKQKQNKRT
          DGLEQGY.VCPSEKR.LLL..TFLKKN.KKKLMVFFS.CMSVKY.Y.LL.YIDL..VLAIHGKQKQNK.T
Retrocopy DGLEQGYFVCPSEKRYLLL<LTFLKKN*KKKLMVFFSACMSVKYPYGLLKYIDL<AVLAIHGKQKQNKHT

Parental  TTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEEL
          TTFF.FCNADSGTLLC.DVAARGLDIPEV.WIVQYDPPDDPKE.IH.V.RTARGLNG..HALLIL.PEEL
Retrocopy TTFF*FCNADSGTLLCKDVAARGLDIPEVNWIVQYDPPDDPKECIHCVRRTARGLNGGRHALLILHPEEL

Parental  GFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLN
          GFL.YLKQSKVPLSEFDFS.SKISDIQSQLEKLIEKNYFLHKSAQEAYKSYI.AYDS.SLKQIFN.NNLN
Retrocopy GFLHYLKQSKVPLSEFDFS*SKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIQAYDSYSLKQIFNINNLN

Parental  LPQVALSFGFKVPPFVDLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISKKSSD-SRQFSH
          LP..ALSFGFK.PPFVDLN.NSNEGKQKK.GG...FGYQKTKKVEKS.IFKHISKKSS..SRQF.H
Retrocopy LPHIALSFGFKLPPFVDLNMNSNEGKQKKQGG---FGYQKTKKVEKSIIFKHISKKSSA<SRQFPH

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	18.52 RPM
SRP007412_cerebellum	0.00 RPM	42.48 RPM
SRP007412_heart	0.00 RPM	23.87 RPM
SRP007412_kidney	0.03 RPM	31.98 RPM
SRP007412_liver	0.00 RPM	26.09 RPM
SRP007412_testis	0.11 RPM	36.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_448 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_448 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_608
Gorilla gorilla	retro_ggor_535

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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,