RetrogeneDB ID: retro_hsap_834

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:130165671..130166948(+)
• Located in intron of: ENSG00000196323

Retrocopy information

• Ensembl ID: ENSG00000255220
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSG00000088205
• Aliases: DDX18, MrDb
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_hsap_834
TTAAAATTCATGCCCAGGAATGCATGCGGAGTCCTTGTTCTCTCACCTACTAGAGAATTAGCCATGCAAATTTTTGGTGT
TCTTAAGGAGCTAAAGACTCACCACGTGCATACCTATGGGTTGATAATGGGTGGCAGTAACGGATCTGCTGAAGCACAGA
AACTTGCTAATGGGATCAACATCACTGTGGCCACACCAGGCCGTCTGCTGTATCATATGCAGAATATCCCAGGGTTTATG
TATAAAAACCTGCAGTGTCTGGTTATTGATGAAGCTGATCGTATCTTGGATGTTGGGTATGAAGAGGAATTAAAGCAAAT
TATTAAACTTTTGCCAACATGTAGACAGACTATGCTCTTTTCTGCCACCCAAACTCGAAAAGTTTTGAAGGTTGGCAAGG
ATTTCTCTGAAAAAAGGAGCCATTGTATGTTAGTGTTGATGATGATAAAGCTAATACAACAGTGGATGGTCTTGAGCAGG
GATATGTTGTTTGTCCTTCTGAAAAGAGATTCCTTCTGCTCTTTACATTCCTTAAGAAGAACCGAAAGAAGCTCGTGGTC
TTCTTTTCATCTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCGTCTTGGCCATTCATGG
AAAGCAAAAGCAAAATAAATGTACGACCACATTCTTCCAGTTCTGCAACACAGATTTGGGAACACATTGTGTACGGATGT
GGTGGCAAGAGGACTGGACATTCCTCAAGTCAACTGGATTGTTCACTATGACCATCCGGATGACCCTAAGGAATATATTC
ATCGTGTAGGTAGAACAGCCAGAGGCCTAAATGGGAGAAGACATGCCTTGCCCATTTTGGGCCCAGAATAATTGGGTTTT
CTTCTACTTGAAACAATCCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCAGTCTCAGC
TTGAGAAATTGATTGAAAAGAACTACTTTCTTTGTAAGTCAGCCCAGGAAGCATATAAGTCATACATATGAGGTTATGAT
TCCCATTCTCTGAAACAGATCTTTAATGTAAATAACTTAAATTTGCCTCAAGTTGCTCTGCCATTTGATTTCAAAGTGCC
TGCCTTTGTTGATCTGAATGTCAATGGCAATGAAGGCAAGCAGAAAAAGCGAGGAGGTGGTGGTGGATTTGACTACCAGA
AAATCAAGAAAGTTGAGAAGTCCAAAATCTTTAAACACATTAGCAAGAAATCATCCGATAGCAGGCAGCTCTCTCAT

Alignment

ORF - retro_hsap_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 63.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLL
          L.FMPRN..GVL.LSPTRELAMQ.FGVLKEL.THHVHTYGLIMGGSN.SAEAQKL.NGINI.VATPGRLL
Retrocopy LKFMPRNACGVLVLSPTRELAMQIFGVLKELKTHHVHTYGLIMGGSNGSAEAQKLANGINITVATPGRLL

Parental  DHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVED-LARISLKK-
          .HMQN.PGFMYKNLQCLVIDEADRILDVG.EEELKQIIKLLPT.RQTMLFSATQTRKV...LARISLKK.
Retrocopy YHMQNIPGFMYKNLQCLVIDEADRILDVGYEEELKQIIKLLPTCRQTMLFSATQTRKVLK>LARISLKK>

Parental  EPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLP
          EPLYV.VDDDKAN.TVDGLEQGYVVCPSEKRFLLLFTFLKKNRKK.L.VFFSSCMSVKYHYELLNYIDLP
Retrocopy EPLYVSVDDDKANTTVDGLEQGYVVCPSEKRFLLLFTFLKKNRKK-LVVFFSSCMSVKYHYELLNYIDLP

Parental  VLAIHGKQKQNKRTTTFFQFCNADSGT-LLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGL
          VLAIHGKQKQNK.TTTFFQFCN.D.GT..LCTDV.ARGLDIP.V.WIV.YD.PDDPKEYIHRVGRTARGL
Retrocopy VLAIHGKQKQNKCTTTFFQFCNTDLGT<TLCTDVVARGLDIPQVNWIVHYDHPDDPKEYIHRVGRTARGL

Parental  NGRGHALLILR-PEELGFLR-YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIR
          NGR.HAL.IL..P...GF...YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFL.KSAQEAYKSYI.
Retrocopy NGRRHALPILG<PRIIGFSS<YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLCKSAQEAYKSYI*

Parental  AYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVNSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHI
          .YDSHSLKQIFNVNNLNLPQVAL.F.FKVP.FVDLNVN.NEGKQKKRGGGGGF.YQK.KKVEKSKIFKHI
Retrocopy GYDSHSLKQIFNVNNLNLPQVALPFDFKVPAFVDLNVNGNEGKQKKRGGGGGFDYQKIKKVEKSKIFKHI

Parental  SKKSSDSRQFSH
          SKKSSDSRQ.SH
Retrocopy SKKSSDSRQLSH

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
bodymap2_adipose	0.00 RPM	86.17 RPM
bodymap2_adrenal	0.29 RPM	106.48 RPM
bodymap2_brain	0.05 RPM	58.67 RPM
bodymap2_breast	0.00 RPM	74.57 RPM
bodymap2_colon	0.00 RPM	91.59 RPM
bodymap2_heart	0.07 RPM	34.01 RPM
bodymap2_kidney	0.06 RPM	69.98 RPM
bodymap2_liver	0.00 RPM	37.73 RPM
bodymap2_lung	0.00 RPM	65.21 RPM
bodymap2_lymph_node	0.00 RPM	64.03 RPM
bodymap2_ovary	0.00 RPM	123.02 RPM
bodymap2_prostate	0.00 RPM	96.02 RPM
bodymap2_skeletal_muscle	0.00 RPM	31.87 RPM
bodymap2_testis	0.04 RPM	84.58 RPM
bodymap2_thyroid	0.19 RPM	144.32 RPM
bodymap2_white_blood_cells	0.00 RPM	141.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_834 was not detected

EST

No EST(s) were mapped for retro_hsap_834 retrocopy.

TSS

No TSS is located nearby retro_hsap_834 retrocopy 5' end.

Lab

retro_hsap_834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_834 has 0 orthologous retrocopies within eutheria group .

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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,