RetrogeneDB - Retrocopy retro_mdom

						
>retro_mdom_358
GTCAGAATTAGTCAGTGCAAATGTACTGCTTCTGAAATAAAACGGATGGAAAAAATTATTTCTGAAAAGTTGCACTATGA

ATTAGAAGCTACTACTGCCTTAAACTTTTTGCACTTAAACCACACTATCATACTTCGTCATACTTCAGAAAGGAAAGAAG

TATCGAGTCTTGATAATGCCTTGATGGAGGCTCAGCTGAAAGCTTGCAATTGCCGACTGATTTTTTCAAAAGCAAAACCG

TCTGTATTAGCCTTCTTAATCTGGAAGTGAAAACTTTGAAATCTATTGAATTATTGGAAATTCGTCTTCTTGTTCTAAAA

CATTCCAGGATTAATGATGCTGATTTCTCTTACTGGACAGAGTTAGTTTCAAAATGCCTACCAGAGTATTCTCCTGAGTG

TTGCAAACCAGACCATAAAAAGCTTGTGTGGATCGTTTCAAGATCTTCACAAAATCTTCACAACAGCTATTACAGTGTCC

CTGTATTGCCTACGATTCCAGAAGGTGGCTGTTTTGAGGAGAGTCAGAGTGAGGACGCTTGTGAAGATTATGAGTTGTGG

AGAAGAATGTCAGAGTAGCTCCCCTCCCAGAGATCAAGAATGCATCTTCGTTTTTGATTTCAAGGTGGCACAAGCCCTGC

GCTTCCAATCT

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:

									ParentalIRISQCKCTASDIKRMEKIISEKLHYELEATTALNFLHLYHTIVLRHTSERKEVLNLDK--LEAQLKACN
		.RISQCKCTAS.IKRMEKIISEKLHYELEATTALNFLHL.HTI.LRHTSERKEV..LD....EAQLKACN
RetrocopyVRISQCKCTASEIKRMEKIISEKLHYELEATTALNFLHLNHTIILRHTSERKEVSSLDNALMEAQLKACN
ParentalCRLI-FSKAKPSVLALCLLNLEVETLKSIELLEILLLVQKHSKINDADFSYWRELVSKCLAEYSSPECCK
		CRLI.F.K.K.......LLNLEV.TLKSIELLEI.LLV.KHS.INDADFSYW.ELVSKCL.EY.SPECCK
RetrocopyCRLI<FFKSK--TVCISLLNLEVKTLKSIELLEIRLLVLKHSRINDADFSYWTELVSKCLPEY-SPECCK
ParentalPDHKKLVWIVSRRTAQNLHNSYYSVPELPTIPEGGCFEESQSEDSCED-MSCGEESLSSSPPSDQECTFF
		PDHKKLVWIVS.R..QNLHNSYYSVP.LPTIPEGGCFEESQSED.CED.MSCGEE..SSSPP.DQEC.F.
RetrocopyPDHKKLVWIVS-RSSQNLHNSYYSVPVLPTIPEGGCFEESQSEDACED>MSCGEECQSSSPPRDQECIFV
ParentalFDFKVAQALCFQS
		FDFKVAQAL.FQS
RetrocopyFDFKVAQALRFQS

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_358 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_358 was not experimentally validated.

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.

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,

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

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

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_mdom_358