RetrogeneDB ID: retro_mdom_358

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:277382471..277383122(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSMODG00000011779
• Aliases: None
• Description: cyclin G2 [Source:HGNC Symbol;Acc:1593]

Sequence

>retro_mdom_358
GTCAGAATTAGTCAGTGCAAATGTACTGCTTCTGAAATAAAACGGATGGAAAAAATTATTTCTGAAAAGTTGCACTATGA
ATTAGAAGCTACTACTGCCTTAAACTTTTTGCACTTAAACCACACTATCATACTTCGTCATACTTCAGAAAGGAAAGAAG
TATCGAGTCTTGATAATGCCTTGATGGAGGCTCAGCTGAAAGCTTGCAATTGCCGACTGATTTTTTCAAAAGCAAAACCG
TCTGTATTAGCCTTCTTAATCTGGAAGTGAAAACTTTGAAATCTATTGAATTATTGGAAATTCGTCTTCTTGTTCTAAAA
CATTCCAGGATTAATGATGCTGATTTCTCTTACTGGACAGAGTTAGTTTCAAAATGCCTACCAGAGTATTCTCCTGAGTG
TTGCAAACCAGACCATAAAAAGCTTGTGTGGATCGTTTCAAGATCTTCACAAAATCTTCACAACAGCTATTACAGTGTCC
CTGTATTGCCTACGATTCCAGAAGGTGGCTGTTTTGAGGAGAGTCAGAGTGAGGACGCTTGTGAAGATTATGAGTTGTGG
AGAAGAATGTCAGAGTAGCTCCCCTCCCAGAGATCAAGAATGCATCTTCGTTTTTGATTTCAAGGTGGCACAAGCCCTGC
GCTTCCAATCT

Alignment

ORF - retro_mdom_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.51 %
• Parental protein coverage: 63.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRISQCKCTASDIKRMEKIISEKLHYELEATTALNFLHLYHTIVLRHTSERKEVLNLDK--LEAQLKACN
          .RISQCKCTAS.IKRMEKIISEKLHYELEATTALNFLHL.HTI.LRHTSERKEV..LD....EAQLKACN
Retrocopy VRISQCKCTASEIKRMEKIISEKLHYELEATTALNFLHLNHTIILRHTSERKEVSSLDNALMEAQLKACN

Parental  CRLI-FSKAKPSVLALCLLNLEVETLKSIELLEILLLVQKHSKINDADFSYWRELVSKCLAEYSSPECCK
          CRLI.F.K.K.......LLNLEV.TLKSIELLEI.LLV.KHS.INDADFSYW.ELVSKCL.EY.SPECCK
Retrocopy CRLI<FFKSK--TVCISLLNLEVKTLKSIELLEIRLLVLKHSRINDADFSYWTELVSKCLPEY-SPECCK

Parental  PDHKKLVWIVSRRTAQNLHNSYYSVPELPTIPEGGCFEESQSEDSCED-MSCGEESLSSSPPSDQECTFF
          PDHKKLVWIVS.R..QNLHNSYYSVP.LPTIPEGGCFEESQSED.CED.MSCGEE..SSSPP.DQEC.F.
Retrocopy PDHKKLVWIVS-RSSQNLHNSYYSVPVLPTIPEGGCFEESQSEDACED>MSCGEECQSSSPPRDQECIFV

Parental  FDFKVAQALCFQS
          FDFKVAQAL.FQS
Retrocopy FDFKVAQALRFQS

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	4.77 RPM	0.00 RPM
SRP007412_cerebellum	1.96 RPM	0.00 RPM
SRP007412_heart	4.78 RPM	0.00 RPM
SRP007412_kidney	3.95 RPM	0.00 RPM
SRP007412_liver	1.51 RPM	0.00 RPM
SRP007412_testis	1.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_358 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_358 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013793	1 retrocopy	retro_amel_960,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Felis catus	ENSFCAG00000026008	1 retrocopy	retro_fcat_1062,
Macropus eugenii	ENSMEUG00000008707	1 retrocopy	retro_meug_1962,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358 ,
Nomascus leucogenys	ENSNLEG00000008169	1 retrocopy	retro_nleu_933,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pan troglodytes	ENSPTRG00000016196	1 retrocopy	retro_ptro_773,
Sus scrofa	ENSSSCG00000008988	1 retrocopy	retro_sscr_813,
Ictidomys tridecemlineatus	ENSSTOG00000027922	1 retrocopy	retro_itri_1112,
Tupaia belangeri	ENSTBEG00000007671	2 retrocopies	retro_tbel_2258, retro_tbel_38,
Tursiops truncatus	ENSTTRG00000014837	1 retrocopy	retro_ttru_491,