RetrogeneDB ID: retro_mmus_688

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:5634138..5634579(+)
• Located in intron of: ENSMUSG00000020481

Retrocopy information

• Ensembl ID: ENSMUSG00000081021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Edf1
• Ensembl ID: ENSMUSG00000015092
• Aliases: Edf1, 0610008L11Rik, AA409425
• Description: endothelial differentiation-related factor 1 [Source:MGI Symbol;Acc:MGI:1891227]

Sequence

>retro_mmus_688
ATGGCCGAGAGTGACTGGGACACCGTGACGGTGCTGTGCAAGAAGGGCCCCACGGCCGCACAGGCCAAGTCTAAGCAGGC
CATCTTAGCAGCTCAGCGACGAGAAGATGTGGAGACATCCAAGAAATGGGCTGCTGGTCAGAACAAGCAGCATTCCATCA
CTAAAAACACAGCCAAGCTAGACTGGGAGACCGAGGAGCTGCATCACGACAGGGTGGCCCTGGAGGTGGGCAAAGTGATC
CAGCGGGGCCGGCAGAGCAAAGGCCTGACCCAGAAGGACCTGGCCACGAAAATCAATGAGAAGCCGCAAGTCATCGCAGA
CTATGAAAGTGGACGGGCCATTCCGAATAACCAGGTTTTGGGCAAAACTGAGAGAGCTATCGGCCTCAAGCTCCGGGGCA
AGGACGTCGGGAAGCCTATCGAGAAGGGGCCGAAGGCGGAA

Alignment

ORF - retro_mmus_688 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAESDWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNKQHSITKNTAKLDRETEELHH
          MAESDWDTVTVL.KKGPTAAQAKSKQAILAAQRR.EDVETSKKWAAGQNKQHSITKNTAKLD.ETEELHH
Retrocopy MAESDWDTVTVLCKKGPTAAQAKSKQAILAAQRR-EDVETSKKWAAGQNKQHSITKNTAKLDWETEELHH

Parental  DRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKDIGKP
          DRV.LEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGK.ERAIGLKLRGKD.GKP
Retrocopy DRVALEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKTERAIGLKLRGKDVGKP

Parental  IEKGPKAK
          IEKGPKA.
Retrocopy IEKGPKAE

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	0.16 RPM	38.74 RPM
SRP007412_cerebellum	0.09 RPM	52.58 RPM
SRP007412_heart	0.34 RPM	73.09 RPM
SRP007412_kidney	0.23 RPM	72.53 RPM
SRP007412_liver	0.25 RPM	81.79 RPM
SRP007412_testis	0.50 RPM	90.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_688 was not detected

EST

No EST(s) were mapped for retro_mmus_688 retrocopy.

TSS

No TSS is located nearby retro_mmus_688 retrocopy 5' end.

Lab

retro_mmus_688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013266	2 retrocopies	retro_amel_1569, retro_amel_996,
Canis familiaris	ENSCAFG00000019544	4 retrocopies	retro_cfam_1283, retro_cfam_1812, retro_cfam_363, retro_cfam_895,
Callithrix jacchus	ENSCJAG00000011166	1 retrocopy	retro_cjac_374,
Erinaceus europaeus	ENSEEUG00000009565	1 retrocopy	retro_eeur_635,
Loxodonta africana	ENSLAFG00000026812	1 retrocopy	retro_lafr_751,
Macropus eugenii	ENSMEUG00000015037	7 retrocopies	retro_meug_108, retro_meug_1742, retro_meug_1805, retro_meug_2070, retro_meug_38, retro_meug_598, retro_meug_773,
Microcebus murinus	ENSMICG00000016498	1 retrocopy	retro_mmur_312,
Macaca mulatta	ENSMMUG00000005051	1 retrocopy	retro_mmul_89,
Monodelphis domestica	ENSMODG00000017329	1 retrocopy	retro_mdom_1713,
Mustela putorius furo	ENSMPUG00000011008	1 retrocopy	retro_mputfur_1377,
Mus musculus	ENSMUSG00000015092	3 retrocopies	retro_mmus_3324, retro_mmus_688 , retro_mmus_809,
Rattus norvegicus	ENSRNOG00000016272	4 retrocopies	retro_rnor_1407, retro_rnor_2005, retro_rnor_2007, retro_rnor_2616,
Sorex araneus	ENSSARG00000007191	1 retrocopy	retro_sara_39,
Tupaia belangeri	ENSTBEG00000014060	4 retrocopies	retro_tbel_1404, retro_tbel_1950, retro_tbel_3538, retro_tbel_967,
Tursiops truncatus	ENSTTRG00000002668	2 retrocopies	retro_ttru_165, retro_ttru_894,