RetrogeneDB ID: retro_pabe_1432

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:12319875..12320214(+)
• Located in intron of: ENSPPYG00000007993

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLT1
• Ensembl ID: ENSPPYG00000017135
• Aliases: None
• Description: dynein, light chain, Tctex-type 1 [Source:HGNC Symbol;Acc:11697]

Sequence

>retro_pabe_1432
ATAGAAGACTACCAGGCTGCGGAGGAGACTGCTTTTGTTGTTGATGAAGTGAGCAAATTGTGAAAGAGGCTATAGAAAGT
GCAGTTGGTGGTAATGCTTATCAACACAGCAAAGTGAACCAGTGGACCACAAATGTAGTTGGAACAAACTTCAAGCCAAC
TCACCAAGCTGGGAAAACCACTTAAATACATTGTGACCTGTGTAATTATGCAAAAGAATGGAGCTGGATTACACATGGCA
AGTTCCTGCTTCTGGGACAGCTCTGCTGACAGGAGCTGCACTGTGCGATGGGAGAATAAAACCATGTACTGCATTGTCGG
CACCTTTGGACTGCGTATT

Alignment

ORF - retro_pabe_1432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEDYQAAEETAFVVDEVSN-IVKEAIESAIGGNAYQHSKVNQWTTNVV-EQTLSQLTKLGKPFKYIVTCV
          .EDYQAAEETAFVVDEVS..IVKEAIESA.GGNAYQHSKVNQWTTNVV.EQT.SQLTKLGKP.KYIVTCV
Retrocopy IEDYQAAEETAFVVDEVSK<IVKEAIESAVGGNAYQHSKVNQWTTNVV>EQTSSQLTKLGKPLKYIVTCV

Parental  IMQKNGAGLHTASSCFWDSSTDGSCTVRWENKTMYCIVSAFGLSI
          IMQKNGAGLH.ASSCFWDSS.D.SCTVRWENKTMYCIV..FGL.I
Retrocopy IMQKNGAGLHMASSCFWDSSADRSCTVRWENKTMYCIVGTFGLRI

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	0.17 RPM	9.51 RPM
SRP007412_cerebellum	0.00 RPM	10.82 RPM
SRP007412_heart	0.06 RPM	31.37 RPM
SRP007412_kidney	0.10 RPM	60.76 RPM
SRP007412_liver	0.18 RPM	21.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1432 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004472	1 retrocopy	retro_btau_220,
Choloepus hoffmanni	ENSCHOG00000003656	1 retrocopy	retro_chof_2043,
Callithrix jacchus	ENSCJAG00000003718	3 retrocopies	retro_cjac_2076, retro_cjac_2301, retro_cjac_2622,
Dipodomys ordii	ENSDORG00000014053	1 retrocopy	retro_dord_60,
Echinops telfairi	ENSETEG00000013883	1 retrocopy	retro_etel_202,
Homo sapiens	ENSG00000146425	2 retrocopies	retro_hsap_1716, retro_hsap_2910,
Gorilla gorilla	ENSGGOG00000009979	3 retrocopies	retro_ggor_1285, retro_ggor_1713, retro_ggor_2015,
Microcebus murinus	ENSMICG00000009483	1 retrocopy	retro_mmur_786,
Myotis lucifugus	ENSMLUG00000001922	2 retrocopies	retro_mluc_111, retro_mluc_282,
Macaca mulatta	ENSMMUG00000019454	2 retrocopies	retro_mmul_1213, retro_mmul_684,
Monodelphis domestica	ENSMODG00000007654	1 retrocopy	retro_mdom_606,
Mus musculus	ENSMUSG00000095677	1 retrocopy	retro_mmus_2882,
Oryctolagus cuniculus	ENSOCUG00000013012	2 retrocopies	retro_ocun_1330, retro_ocun_1599,
Otolemur garnettii	ENSOGAG00000000494	2 retrocopies	retro_ogar_1176, retro_ogar_2889,
Pongo abelii	ENSPPYG00000017135	2 retrocopies	retro_pabe_1432 , retro_pabe_2424,
Pongo abelii	ENSPPYG00000020241	2 retrocopies	retro_pabe_1804, retro_pabe_2098,
Pan troglodytes	ENSPTRG00000018746	2 retrocopies	retro_ptro_1230, retro_ptro_1966,
Ictidomys tridecemlineatus	ENSSTOG00000006273	1 retrocopy	retro_itri_1269,
Tarsius syrichta	ENSTSYG00000003114	1 retrocopy	retro_tsyr_236,
Tursiops truncatus	ENSTTRG00000011340	2 retrocopies	retro_ttru_912, retro_ttru_942,