RetrogeneDB ID: retro_pabe_744

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:127473515..127474657(+)
• Located in intron of: ENSPPYG00000004067

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSPPYG00000012796
• Aliases: None
• Description: ATP-dependent RNA helicase DDX18 [Source:RefSeq peptide;Acc:NP_001126280]

Sequence

>retro_pabe_744
TTAAAATTCATGCCCAGGAATGCATCGGGAGTCCTTGTTCTCTCACCCACTAGAGAATTAGCCATGCAAATTTTTGGTGT
TCTTAAGGAGCTAATGACTCACCACGTGCATACCCTACGGATTGATAATGGGTGGCAGTAACAGATCTGCTGAAGCACAG
AAACCTGCTAATGGGATCAACATCACTGCGGCCACACCAGGCCGTCTGCTGTACCACATGCAGAATATCCCAGGGTTTAT
GTATAAAAACCTGCAGTGTCTGGTTATTGATGAAGCTGATCGTATCTTGGATGATGGGTTTGAAGAGCAATTAAAGCAAA
TTATTAAACTTTTGCCAACATGTAGACAGACTATGCTCTTTTCTGCCACCCAAACTCGAAAAGTTGAAGGCCTGGCAAGG
ATTTCTCTGAAAAAGGAGCCATTGTATGTTGGTGTTGATGATGATAAAGCTAATGCAACAGTGGATGGTCTTGAGCAGGG
ATATGTTGTTTGTCCTTCTGAAAAGAGATTCCTTCTACTCTTTACATTCCTTAAGAAGAACCGAAAGAAGCTCGTGGTCT
TCTTTTCCTCTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCATCTTGGCCATTCATGGA
AAGCAAAAGCAAAATAAATGTACAACCACATTCTTCCAGTTCTGCAACGCAGATTCGGGAACACTATTGTGTACGGATAT
GGTGGCAAGAGGACTGGACATTCCTCAAGTCGACTGGATTGTTCACTATGACCATCCGGATGACCCTAAGGAATATATTC
ATCGTGTAGGTAGAACAGCCAGAGGCCTAAATGGGAGAAGACATGCCTTGCCCATTTTGGGCCCAGAAGAATTGGGTTTT
CTTCTACTTGAAACAATCCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCAGTCTCAGC
TTGAGAAATTGATTGAAAAGAACTGCTTTCTTTGTAAGTCAGCCCAGGAAGCATATAAGTCATACATACGAGGTTATGAT
TCCCATTCTCTGAAACAGATCTTTAATGTAAATAACTTAAATTTGCCTCAAGTTGCTCTGCCATTTGATTTCAAAGTGCC
TGCCTTTGTTGATCTGAACGTC

Alignment

ORF - retro_pabe_744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.61 %
• Parental protein coverage: 61.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHT-YGLIMGGSNRSAEAQKLANGINIIVATPGRL
          L.FMPRN..GVL.LSPTRELAMQ.FGVLKELMTHHVHT.YGLIMGGSNRSAEAQK.ANGINI..ATPGRL
Retrocopy LKFMPRNASGVLVLSPTRELAMQIFGVLKELMTHHVHT>YGLIMGGSNRSAEAQKPANGINITAATPGRL

Parental  LDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKE
          L.HMQN.PGFMYKNLQCLVIDEADRILD.GFEE.LKQIIKLLPT.RQTMLFSATQTRKVE.LARISLKKE
Retrocopy LYHMQNIPGFMYKNLQCLVIDEADRILDDGFEEQLKQIIKLLPTCRQTMLFSATQTRKVEGLARISLKKE

Parental  PLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPV
          PLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKK.L.VFFSSCMSVKYHYELLNYIDLP.
Retrocopy PLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKK-LVVFFSSCMSVKYHYELLNYIDLPI

Parental  LAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNG
          LAIHGKQKQNK.TTTFFQFCNADSGTLLCTD..ARGLDIP.VDWIV.YD.PDDPKEYIHRVGRTARGLNG
Retrocopy LAIHGKQKQNKCTTTFFQFCNADSGTLLCTDMVARGLDIPQVDWIVHYDHPDDPKEYIHRVGRTARGLNG

Parental  RGHALLILRPEE-LGFLR-YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAY
          R.HAL.IL.PEE..GF...YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKN.FL.KSAQEAYKSYIR.Y
Retrocopy RRHALPILGPEE<IGFSS<YLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNCFLCKSAQEAYKSYIRGY

Parental  DSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLSI
          DSHSLKQIFNVNNLNLPQVAL.F.FKVP.FVDL..
Retrocopy DSHSLKQIFNVNNLNLPQVALPFDFKVPAFVDLNV

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	13.66 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.00 RPM	8.22 RPM
SRP007412_kidney	0.07 RPM	10.61 RPM
SRP007412_liver	0.00 RPM	12.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_744 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_744 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,