RetrogeneDB ID: retro_mmus_4

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:69182815..69183136(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000049751
• Aliases: Rpl36al, 2410038A03Rik, RPL36A
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rpl36a
• Ensembl ID: ENSMUSG00000079435
• Aliases: Rpl36a, L44L, Rpl44
• Description: ribosomal protein L36A [Source:MGI Symbol;Acc:MGI:1201789]

Sequence

>retro_mmus_4
ATGGTCAACGTACCAAAAACCCGAAGGACTTTCTGTAAGAAATGTGGCAAGCATCAGCCTCACAAAGTGACCCAGTATAA
GAAGGGCAAGGATTCCCTGTATGCCCAAGGAAAGCGGCGCTACGATCGCAAGCAGAGTGGCTACGGTGGGCAGACAAAGC
CAATCTTTCGAAAGAAGGCCAAAACCACAAAGAAGATTGTGCTCAGGCTTGAGTGTGTTGAGCCCAACTGCAGATCCAAG
AGGATGCTGGCCATTAAGAGATGCAAGCATTTTGAACTGGGAGGCGACAAGAAGAGGAAGGGCCAAGTGATCCAGTTCTA
A

Alignment

ORF - retro_mmus_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
          MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
Retrocopy MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL

Parental  ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
Retrocopy ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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	7.45 RPM	42.61 RPM
SRP007412_cerebellum	7.21 RPM	34.48 RPM
SRP007412_heart	15.47 RPM	52.36 RPM
SRP007412_kidney	22.71 RPM	55.69 RPM
SRP007412_liver	32.82 RPM	58.55 RPM
SRP007412_testis	20.08 RPM	7.87 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_4 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	12:69183686..69184519
ENCFF001YIJ	POLR2A	12:69183311..69184924
ENCFF001YKA	POLR2A	12:69183179..69185647

EST

No EST(s) were mapped for retro_mmus_4 retrocopy.

TSS

No TSS is located nearby retro_mmus_4 retrocopy 5' end.

Lab

retro_mmus_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_4 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2
Gorilla gorilla	retro_ggor_208
Pongo abelii	retro_pabe_55
Callithrix jacchus	retro_cjac_55
Bos taurus	retro_btau_92
Equus caballus	retro_ecab_204

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens	ENSG00000241343	14 retrocopies	retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2, retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mus musculus	ENSMUSG00000079435	1 retrocopy	retro_mmus_4 ,
Pongo abelii	ENSPPYG00000025837	37 retrocopies	retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011, retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Ictidomys tridecemlineatus	ENSSTOG00000027251	20 retrocopies	retro_itri_1171, retro_itri_1189, retro_itri_1364, retro_itri_1405, retro_itri_1471, retro_itri_161, retro_itri_1681, retro_itri_290, retro_itri_385, retro_itri_430, retro_itri_555, retro_itri_609, retro_itri_644, retro_itri_730, retro_itri_753, retro_itri_784, retro_itri_803, retro_itri_845, retro_itri_865, retro_itri_903,