RetrogeneDB ID: retro_mmus_3101

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:4652063..4652477(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam136a
• Ensembl ID: ENSMUSG00000057497
• Aliases: Fam136a, 2010309E21Rik, AW124904, Hyccin
• Description: family with sequence similarity 136, member A [Source:MGI Symbol;Acc:MGI:1913738]

Sequence

>retro_mmus_3101
ATAGCGGAGGTGCAGCAACTCCGAGTGCAGGAGGCTGTGGACGCCATGGTGAAAAGTGTGGAGAGAGAGAACATCCGGAA
GATGCAGGGCCTCATGTTCCGGTGCAGCGCCAACTGCTGTGAAGACACCCAAGCATCTATGCAGCAGGTGCACCAATGCA
TCGAGAGCTGCCATGCGCCTCTGGCTCAAGCCCAGGCTCTGGTCACCAGCGAGCTGGAAAGGTTCCAGGACCGCCTGGCC
CGCTGCACCATGCATTGCAATGACAAAGCCAAAGACTCAATGGATGCAGGAACTATGGAGCTTCAGGTGAAGCGACAGCT
AGACAGATGTGTGGCCAAGTGTGTGGATGACCATATGCACCTCATCCCAACAATGACCAAGAAGATGAAGGAGTCTCTGT
CATCCATCGGGAAA

Alignment

ORF - retro_mmus_3101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVQQLRVQEAVDAMVKSVERENIRKMQGLMFRCSANCCEDTQASMQQVHQCIERCHAPLAQAQALVTS
          .AEVQQLRVQEAVDAMVKSVERENIRKMQGLMFRCSANCCEDTQASMQQVHQCIE.CHAPLAQAQALVTS
Retrocopy IAEVQQLRVQEAVDAMVKSVERENIRKMQGLMFRCSANCCEDTQASMQQVHQCIESCHAPLAQAQALVTS

Parental  ELERFQDRLARCTMHCNDKAKDSMDAGTKELQVKRQLDSCVTKCVDDHMHLIPTMTKKMKESLSSIGK
          ELERFQDRLARCTMHCNDKAKDSMDAGT.ELQVKRQLD.CV.KCVDDHMHLIPTMTKKMKESLSSIGK
Retrocopy ELERFQDRLARCTMHCNDKAKDSMDAGTMELQVKRQLDRCVAKCVDDHMHLIPTMTKKMKESLSSIGK

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	0.09 RPM	13.34 RPM
SRP007412_cerebellum	0.09 RPM	7.03 RPM
SRP007412_heart	0.00 RPM	18.06 RPM
SRP007412_kidney	0.06 RPM	15.78 RPM
SRP007412_liver	0.05 RPM	35.64 RPM
SRP007412_testis	0.14 RPM	7.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3101 was not detected

EST

1 EST(s) were mapped to retro_mmus_3101 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI159000	4652071	4652173	97.1	99	3	96

TSS

No TSS is located nearby retro_mmus_3101 retrocopy 5' end.

Lab

retro_mmus_3101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3101 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015992	1 retrocopy	retro_amel_1454,
Bos taurus	ENSBTAG00000008674	2 retrocopies	retro_btau_37, retro_btau_88,
Canis familiaris	ENSCAFG00000003353	2 retrocopies	retro_cfam_1042, retro_cfam_148,
Cavia porcellus	ENSCPOG00000009117	1 retrocopy	retro_cpor_221,
Dasypus novemcinctus	ENSDNOG00000019447	7 retrocopies	retro_dnov_2036, retro_dnov_2465, retro_dnov_2612, retro_dnov_324, retro_dnov_620, retro_dnov_873, retro_dnov_901,
Dipodomys ordii	ENSDORG00000006529	4 retrocopies	retro_dord_365, retro_dord_391, retro_dord_733, retro_dord_778,
Felis catus	ENSFCAG00000008119	1 retrocopy	retro_fcat_1459,
Homo sapiens	ENSG00000035141	5 retrocopies	retro_hsap_1855, retro_hsap_2599, retro_hsap_2683, retro_hsap_3136, retro_hsap_3413,
Gorilla gorilla	ENSGGOG00000023247	6 retrocopies	retro_ggor_1361, retro_ggor_1625, retro_ggor_2155, retro_ggor_2356, retro_ggor_53, retro_ggor_8,
Loxodonta africana	ENSLAFG00000002304	1 retrocopy	retro_lafr_146,
Macropus eugenii	ENSMEUG00000015791	8 retrocopies	retro_meug_1126, retro_meug_1351, retro_meug_1545, retro_meug_167, retro_meug_2131, retro_meug_219, retro_meug_457, retro_meug_719,
Macaca mulatta	ENSMMUG00000007962	5 retrocopies	retro_mmul_1421, retro_mmul_1772, retro_mmul_220, retro_mmul_327, retro_mmul_656,
Monodelphis domestica	ENSMODG00000011533	1 retrocopy	retro_mdom_65,
Mus musculus	ENSMUSG00000057497	2 retrocopies	retro_mmus_240, retro_mmus_3101 ,
Otolemur garnettii	ENSOGAG00000028265	4 retrocopies	retro_ogar_1788, retro_ogar_2273, retro_ogar_379, retro_ogar_684,
Pongo abelii	ENSPPYG00000012323	6 retrocopies	retro_pabe_1512, retro_pabe_1917, retro_pabe_2297, retro_pabe_2618, retro_pabe_2828, retro_pabe_3032,
Pan troglodytes	ENSPTRG00000012030	6 retrocopies	retro_ptro_1237, retro_ptro_1523, retro_ptro_1809, retro_ptro_2120, retro_ptro_2318, retro_ptro_3063,
Rattus norvegicus	ENSRNOG00000016273	1 retrocopy	retro_rnor_1679,
Sus scrofa	ENSSSCG00000026446	6 retrocopies	retro_sscr_1075, retro_sscr_229, retro_sscr_230, retro_sscr_309, retro_sscr_335, retro_sscr_914,
Ictidomys tridecemlineatus	ENSSTOG00000008343	1 retrocopy	retro_itri_1026,
Tupaia belangeri	ENSTBEG00000017418	8 retrocopies	retro_tbel_1377, retro_tbel_1875, retro_tbel_2479, retro_tbel_2516, retro_tbel_3373, retro_tbel_3703, retro_tbel_401, retro_tbel_999,
Tursiops truncatus	ENSTTRG00000001198	5 retrocopies	retro_ttru_1110, retro_ttru_1771, retro_ttru_1903, retro_ttru_396, retro_ttru_550,