RetrogeneDB ID: retro_mdom_1018

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:228425687..228426264(+)
• Located in intron of: ENSMODG00000020267

Retrocopy information

• Ensembl ID: ENSMODG00000024857
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSMODG00000007651
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_mdom_1018
TACAAACCAGAGTCCTCAACAGAGGAGGAGAAAAATGCCCCATTAGCACTGATCTCATCCAAATAAGCCAATATAAATTC
ATTGTTTTTGATCTGATGAGAATGGAAAAGATTGTAATGGAGAAGGTGTGTTGGAAAGTCAAAGCTACTACTGCCTTTCA
GTTTCTGCAACTCTATTATTCACTCATTCATGAAAACTTATCATTTGAAAGGAGAAAGAACCTGAATTTTGAGAGGCTGG
AAGCTCAGCTTAAGGCAGGCCACTGTACAATTATGTTTTCTAAATCAAAGTCTTCTGTATTGGCATTGTCTATAGCTGCA
CTAGAAGTTCAAGCACCGAAGCTTATTGAATTGACCGAAGGAATAGAATGCCTTCAGAAACCTTCCAAGATAAATTGCAG
AGATCTGACCTTCTGGCAGAAACTTGTAGCAAAGTGCCTAACTGAATACTCATCAAACAAGTGTTCTAAACCAAATCTTC
AGAATTGAAGTCGATCGTGTCTGGGTGTTCTGCACGTCAGTTGAAACATAGTTATTACAAAATCACTCATCTTCCAACAG
TCCTTGAAACTGTGTCT

Alignment

ORF - retro_mdom_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 65.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YLAVKSTEEERNVPLA-TDLIRISQYKFTVSDLMRMEKIVLEKVCWKVKATTAFQFLQLYYSLIHENLPF
          Y....STEEE.N.PLA.TDLI.ISQYKF.V.DLMRMEKIV.EKVCWKVKATTAFQFLQLYYSLIHENL.F
Retrocopy YKPESSTEEEKNAPLA<TDLIQISQYKFIVFDLMRMEKIVMEKVCWKVKATTAFQFLQLYYSLIHENLSF

Parental  ERRKNLSFERLEAQLKACHCRIMFSKAKPSVLALSIIALEVQAQKFIELTEGIECLQKHSKINCRDLTFW
          ERRKNL.FERLEAQLKA.HC.IMFSK.K.SVLALSI.ALEVQA.K.IELTEGIECLQK.SKINCRDLTFW
Retrocopy ERRKNLNFERLEAQLKAGHCTIMFSKSKSSVLALSIAALEVQAPKLIELTEGIECLQKPSKINCRDLTFW

Parental  QELVAKCLTEYSSNKCSKPNVQ-KLKWIVSGRTARQLKHSYYKITHLPTIPETGS
          Q.LVAKCLTEYSSNKCSKPN.Q..LK.IVSG..ARQLKHSYYKITHLPT..ET.S
Retrocopy QKLVAKCLTEYSSNKCSKPNLQ<ELKSIVSGCSARQLKHSYYKITHLPTVLETVS

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	195.13 RPM
SRP007412_cerebellum	0.00 RPM	156.05 RPM
SRP007412_heart	0.00 RPM	982.80 RPM
SRP007412_kidney	0.00 RPM	1839.62 RPM
SRP007412_liver	0.00 RPM	173.70 RPM
SRP007412_testis	0.00 RPM	209.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1018 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1018 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 18 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018 ,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,