RetrogeneDB ID: retro_mmus_2994

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:11253802..11254136(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Max
• Ensembl ID: ENSMUSG00000059436
• Aliases: Max, AA960152, AI875693, bHLHd4, bHLHd5, bHLHd6, bHLHd7, bHLHd8
• Description: Max protein [Source:MGI Symbol;Acc:MGI:96921]

Sequence

>retro_mmus_2994
GTGAGTGATTACAATGACATCAAGGTAGACAGAAAAGCTGACAAGAAGGCTCAGCATAATGCAATGAAATGAAAATGTAG
GGACCACATCAAAGACAGCTTTAACCATTTGCAGAGCTTATTTACATTACTCCAAGGAGAGAATGGCATCCTGGGCTCAA
ATCCTAGACAAAGCAACAGAGTATATCCAATATGTGCAAAGGAAAAACCATACACACCAGCAAGACATTGATGACCTCAA
GAGGCAGGATGCTTTTCTGGAGCAACAAGTCCGTGCACTGGAGAAAGCAAGATCAAATGCCCAACTGCAGACCAACTACC
CCTCCTCAGACAAC

Alignment

ORF - retro_mmus_2994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.11 %
• Parental protein coverage: 73.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDNDDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEK-ASRAQILDKATEYIQYMRRKN
          .SD..DI.V...ADK.A.HNA...K.RDHIKDSF..L......LQGE..AS.AQILDKATEYIQY..RKN
Retrocopy VSDYNDIKVDRKADKKAQHNAMK*KCRDHIKDSFNHLQSLFTLLQGEN>ASWAQILDKATEYIQYVQRKN

Parental  HTHQQDIDDLKRQNALLEQQVRALEKARSSAQLQTNYPSSDN
          HTHQQDIDDLKRQ.A.LEQQVRALEKARS.AQLQTNYPSSDN
Retrocopy HTHQQDIDDLKRQDAFLEQQVRALEKARSNAQLQTNYPSSDN

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	40.65 RPM
SRP007412_cerebellum	0.00 RPM	92.92 RPM
SRP007412_heart	0.00 RPM	38.23 RPM
SRP007412_kidney	0.00 RPM	49.09 RPM
SRP007412_liver	0.00 RPM	22.34 RPM
SRP007412_testis	0.00 RPM	11.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2994 was not detected

EST

No EST(s) were mapped for retro_mmus_2994 retrocopy.

TSS

No TSS is located nearby retro_mmus_2994 retrocopy 5' end.

Lab

retro_mmus_2994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2994 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994 ,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,