RetrogeneDB ID: retro_mmus_1360

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:77811970..77812167(+)
• Located in intron of: ENSMUSG00000022443

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl37
• Ensembl ID: ENSMUSG00000041841
• Aliases: Rpl37, 3110005M08Rik
• Description: ribosomal protein L37 [Source:MGI Symbol;Acc:MGI:1914531]

Sequence

>retro_mmus_1360
AGAGCCCACTGTGGCAAGTATGGCCCTGCCAAATGCGAAGGAAAATATAACTGGAGTGGCAAGGCTGAAAGGCAAAATGA
TCCCGGGGCCAGCAAATGAGGCCCCTAAAAATTGTCTATGGCAGATTCAGGCATGGAGTTTGTGATGGAGAAATATCTAA
GCCCAAGAGGGCAGCGGATGCAGCATCGGCTTCATCT

Alignment

ORF - retro_mmus_1360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.29 %
• Parental protein coverage: 69.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGR-MRHLKIVYRRFRHGFREGTTPKPKRAAVAASSSS
          ...CGK.G.PAK...KYNWS.KA.R.N..G....MR.LKIVY.RFRHG...G...KPKRAA.AAS.SS
Retrocopy RAHCGKYG-PAKCEGKYNWSGKAERQNDPGASK<MRPLKIVYGRFRHGVCDGEISKPKRAADAASASS

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	65.70 RPM
SRP007412_cerebellum	0.00 RPM	37.21 RPM
SRP007412_heart	0.03 RPM	58.93 RPM
SRP007412_kidney	0.02 RPM	45.29 RPM
SRP007412_liver	0.00 RPM	67.59 RPM
SRP007412_testis	0.00 RPM	51.18 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1360 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	15:77809933..77811344
ENCFF001XVA	POLR2A	15:77811411..77811823
ENCFF001YKA	POLR2A	15:77811482..77811617

EST

No EST(s) were mapped for retro_mmus_1360 retrocopy.

TSS

No TSS is located nearby retro_mmus_1360 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GCTTTAGCAGCATATTCAAAC (21 nt long)
• Reverse primer: ACATTGTTTTATGATTGATCAG (22 nt long)
• Annealing temperature: 50 °C
• (Expected) product size: 402
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1360 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005142	6 retrocopies	retro_btau_1430, retro_btau_1502, retro_btau_1575, retro_btau_1670, retro_btau_181, retro_btau_243,
Callithrix jacchus	ENSCJAG00000007388	10 retrocopies	retro_cjac_107, retro_cjac_1443, retro_cjac_169, retro_cjac_2091, retro_cjac_2443, retro_cjac_247, retro_cjac_2495, retro_cjac_2654, retro_cjac_2956, retro_cjac_332,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Mus musculus	ENSMUSG00000041841	28 retrocopies	retro_mmus_1333, retro_mmus_1360 , retro_mmus_1425, retro_mmus_1560, retro_mmus_1717, retro_mmus_1732, retro_mmus_1804, retro_mmus_1813, retro_mmus_2067, retro_mmus_2379, retro_mmus_2385, retro_mmus_2513, retro_mmus_2559, retro_mmus_2575, retro_mmus_2691, retro_mmus_2811, retro_mmus_2838, retro_mmus_3090, retro_mmus_3222, retro_mmus_3343, retro_mmus_3345, retro_mmus_3364, retro_mmus_3455, retro_mmus_3493, retro_mmus_3503, retro_mmus_3504, retro_mmus_3674, retro_mmus_438,
Oryctolagus cuniculus	ENSOCUG00000029674	11 retrocopies	retro_ocun_1063, retro_ocun_1269, retro_ocun_1476, retro_ocun_1491, retro_ocun_1514, retro_ocun_1870, retro_ocun_295, retro_ocun_683, retro_ocun_771, retro_ocun_879, retro_ocun_956,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,
Sus scrofa	ENSSSCG00000025883	5 retrocopies	retro_sscr_1004, retro_sscr_1220, retro_sscr_1221, retro_sscr_767, retro_sscr_872,