RetrogeneDB ID: retro_pabe_1804

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:12480365..12480712(-)
• Located in intron of: ENSPPYG00000010725

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLT3
• Ensembl ID: ENSPPYG00000020241
• Aliases: None
• Description: Dynein light chain Tctex-type 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVF5]

Sequence

>retro_pabe_1804
ATGGAGGAGTGCCATCGCCACTGCGACGAGGTTGGCCTCAATGCTGAGGAAGCGCACAATATTGTCAAAGAGTGTGCAGA
TGGGGTTTAAGGTGGTGAAGATTATAATTACAACAACATCAACCAGTGCACCACAAGCATAGTAGCATAATCGTTAACAC
ATCTGGTTAAGTTGGGAAAAGCTTATAAATGTATTATGAACTGTGCAGTGGTCCAGAAGAGCGCATATGGCTTTCGCACA
GCAGCTCCTGTTTTTGGGATACCACATCTGATGGAATCTGTACTGTAAGATGGGAGAAGGGGACCATGAACTGAATTGTC
AATGTTTTTGCCATTGCTGTTGTTCTT

Alignment

ORF - retro_pabe_1804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEYHRHCDEVGFNAEEAHNIVKECVDGVLGGEDYNHNNINQWTASIVEQSLTHLVKLGKAYKYIVTCAV
          MEE.HRHCDEVG.NAEEAHNIVKEC.DGV.GGEDYN.NNINQ.T.SIV..SLTHLVKLGKAYK.I..CAV
Retrocopy MEECHRHCDEVGLNAEEAHNIVKECADGV*GGEDYNYNNINQCTTSIVA*SLTHLVKLGKAYKCIMNCAV

Parental  VQKSAYGFHTA-SSCFWDTTSDGTCTVRWENRTMNCIVNVFAIAIVL
          VQKSAYGF.TA.SSCFWDTTSDG.CTVRWE..TMN.IVNVFAIA.VL
Retrocopy VQKSAYGFRTA<SSCFWDTTSDGICTVRWEKGTMN*IVNVFAIAVVL

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	0.06 RPM	16.64 RPM
SRP007412_cerebellum	0.00 RPM	19.33 RPM
SRP007412_heart	0.00 RPM	8.28 RPM
SRP007412_kidney	0.00 RPM	8.35 RPM
SRP007412_liver	0.00 RPM	10.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1804 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1804 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2453
Pan troglodytes	retro_ptro_1417

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038156	1 retrocopy	retro_btau_907,
Canis familiaris	ENSCAFG00000013955	1 retrocopy	retro_cfam_1778,
Callithrix jacchus	ENSCJAG00000005227	1 retrocopy	retro_cjac_1247,
Cavia porcellus	ENSCPOG00000001932	1 retrocopy	retro_cpor_91,
Dasypus novemcinctus	ENSDNOG00000014826	1 retrocopy	retro_dnov_1638,
Felis catus	ENSFCAG00000026355	1 retrocopy	retro_fcat_1736,
Homo sapiens	ENSG00000165169	2 retrocopies	retro_hsap_2152, retro_hsap_2453,
Macropus eugenii	ENSMEUG00000013924	4 retrocopies	retro_meug_1294, retro_meug_1443, retro_meug_33, retro_meug_620,
Microcebus murinus	ENSMICG00000001440	1 retrocopy	retro_mmur_556,
Myotis lucifugus	ENSMLUG00000015093	1 retrocopy	retro_mluc_739,
Macaca mulatta	ENSMMUG00000013221	1 retrocopy	retro_mmul_660,
Monodelphis domestica	ENSMODG00000021109	7 retrocopies	retro_mdom_1023, retro_mdom_1145, retro_mdom_1432, retro_mdom_1745, retro_mdom_1748, retro_mdom_376, retro_mdom_935,
Mus musculus	ENSMUSG00000031176	1 retrocopy	retro_mmus_3147,
Nomascus leucogenys	ENSNLEG00000000985	2 retrocopies	retro_nleu_1900, retro_nleu_821,
Oryctolagus cuniculus	ENSOCUG00000009787	1 retrocopy	retro_ocun_836,
Pongo abelii	ENSPPYG00000017135	2 retrocopies	retro_pabe_1432, retro_pabe_2424,
Pongo abelii	ENSPPYG00000020241	2 retrocopies	retro_pabe_1804 , retro_pabe_2098,
Pan troglodytes	ENSPTRG00000021793	1 retrocopy	retro_ptro_1417,
Rattus norvegicus	ENSRNOG00000003611	2 retrocopies	retro_rnor_1462, retro_rnor_652,
Sarcophilus harrisii	ENSSHAG00000008069	2 retrocopies	retro_shar_141, retro_shar_825,
Tupaia belangeri	ENSTBEG00000014383	2 retrocopies	retro_tbel_3460, retro_tbel_885,
Vicugna pacos	ENSVPAG00000006367	1 retrocopy	retro_vpac_246,