RetrogeneDB ID: retro_mdom_1917

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:129758706..129759865(-)
• Located in intron of: ENSMODG00000016726

Retrocopy information

• Ensembl ID: ENSMODG00000016729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSMODG00000001303
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_mdom_1917
ATCCCAGCTTTTTCCCTTTTGAAAACACTAAGAATAATGTCCTTACATCAATTTTTACTAGAGCCAATCACCTGCCATGC
TTGGAACAGAGACCATACCCATTCTTACTTGGAGATTGCCCTTAGCCCTAATAATCATGAAGTCCACATCTACAAGAAGA
ATGGGAAACAATGGATGAAAGCCCATGAACTGAAGGAACACAATGGACACATCACAGGTATTGCCTGGGCTCCCAAGAGC
AATCGCATTTTAACTTGTGGGGCAGACTGCAATGCCTATGTCTGGAGTCAGAAAGATGGAATCTGGAAGCCAACCTTGGT
GATATTGAGGATTAATCGTGCAGCTACCTTTGTGAAATGGTCTCCCTTAGAGAATAAATTTGCTGTAGGTAGTGGAGCTC
AACTGATTTCTGTGTGCTACTTTGAGTCTGAAAATGACTGGTGGGTGAGCAAACACATAAAAAAGCCAATTCATTCTACT
GTCCTTAGTTTGGACTGGCACCCCAACAATGTTTTGCTGGCTGCTGGATCTTGTGACTTCAAATGCAGAGTATATTCTGC
CTACATTAAAGAAGTTGATGAAAAACCAGCCAATTCTCCATGGGGTACCAAGATGCCTTTTGGTCAGCTGATGTCAGGAG
TTTGGTGGTACTGAAAGTGGTGGTTGGGTCCATGGGGTCAGTTTCTCTGCCAGTGGGAACCGCCTCGCTTGGGTCAGCCA
TGATAGTACTGTATCAGTTGTTGATGCCTCTAAAAACATGATGGTTTCACAGCTGAAAACAGAGTTCCTCCCATTCCTGA
GTGTGTCATTTGTCTCTGAGAATAGTGTGGTGGCTGCTGGCCATGACTGCTGCCTGATGCTGTTTAATTATGATGATTGT
GGCCCCTTGACCTTCATCTCCAAATTAGACATTCCAAAAGAGAGCACTCAGTGCAACATCTCTGCCATGGAATGCTTCTG
CAACATGGACAAGAGAGCCACAACCGAGGATCACAACACTGCTCTAGACACACTACACCAAAACAGCATCGCCCAAATGT
CTATTTATGAAGTGGACAAGCAAGAATGCTGCAAATTTTGCACCACTGGCATTGATGGAGCTATGACAATTTGGGATTCC
AAGACTTTAAAGTCTTTGATCCAGGGACTATGACTCATG

Alignment

ORF - retro_mdom_1917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISAFSLLKTLRIMSLHQFLLEPITCHAWNRDRT----QIALSPNNHEVHIYKKNGNQWMKAHELKEHNGH
          I.AFSLLKTLRIMSLHQFLLEPITCHAWNRD.T.....IALSPNNHEVHIYKKNG.QWMKAHELKEHNGH
Retrocopy IPAFSLLKTLRIMSLHQFLLEPITCHAWNRDHTHSYLEIALSPNNHEVHIYKKNGKQWMKAHELKEHNGH

Parental  ITGIDWAPKSDRIVTCGADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCY
          ITGI.WAPKS.RI.TCGAD.NAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGA.LISVCY
Retrocopy ITGIAWAPKSNRILTCGADCNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGAQLISVCY

Parental  FESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGTKMPFGQL
          FESENDWWVSKHIKKPI.STVLSLDWHPNNVLLAAGSCDFKCRV.SAYIKEVDEKPA..PWGTKMPFGQL
Retrocopy FESENDWWVSKHIKKPIHSTVLSLDWHPNNVLLAAGSCDFKCRVYSAYIKEVDEKPANSPWGTKMPFGQL

Parental  MS-EFGGTGSGGWVHGVSFSASGNRLAWVSHDSTVSVADASKNMMVSQLKTEFLPLLSVSFVSENSVVAA
          MS.EFGGT.SGGWVHGVSFSASGNRLAWVSHDSTVSV.DASKNMMVSQLKTEFLP.LSVSFVSENSVVAA
Retrocopy MS>EFGGTESGGWVHGVSFSASGNRLAWVSHDSTVSVVDASKNMMVSQLKTEFLPFLSVSFVSENSVVAA

Parental  GHDCCPMLFNYDDRGPLTFVSKLDIPKQSIQRNISAMERFRNMDKRATTEDRNTALDTLHQNSITQVSIY
          GHDCC.MLFNYDD.GPLTF.SKLDIPK.S.Q.NISAME.F.NMDKRATTED.NTALDTLHQNSI.Q.SIY
Retrocopy GHDCCLMLFNYDDCGPLTFISKLDIPKESTQCNISAMECFCNMDKRATTEDHNTALDTLHQNSIAQMSIY

Parental  EVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
          EVDKQ.C.KFCTTGIDGAMTIWD.KTL.S.IQGL..M
Retrocopy EVDKQECCKFCTTGIDGAMTIWDSKTLKSLIQGL*LM

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1917 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1917 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dasypus novemcinctus	ENSDNOG00000005984	5 retrocopies	retro_dnov_1615, retro_dnov_1839, retro_dnov_1966, retro_dnov_2257, retro_dnov_941,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917 , retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Sus scrofa	ENSSSCG00000007609	1 retrocopy	retro_sscr_387,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,
Tursiops truncatus	ENSTTRG00000003002	4 retrocopies	retro_ttru_1621, retro_ttru_1838, retro_ttru_575, retro_ttru_853,