RetrogeneDB ID: retro_mmus_1234

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:119278423..119279086(+)
• Located in intron of: ENSMUSG00000053465

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam60a
• Ensembl ID: ENSMUSG00000039985
• Aliases: Fam60a, Ppcs1, Pptcs1, Tera
• Description: family with sequence similarity 60, member A [Source:MGI Symbol;Acc:MGI:1929091]

Sequence

>retro_mmus_1234
ATGTTTGGTTTTCACAAGCCAAAGATGTACCGAAGTATAGAGGGCTGCTGTATATGCAGAGCCAAGTCCTCCAGCTCCCG
GTTCACGGACAGTAAACGTTACGAAAAGGACTTCCAGAGCTGTTTTGGGTTGCATGAGACTCGCTCAGGAGACATCTGTA
ATGCCTGTGTGCTGCTTGTGAAAAGATGGAAGAAGTTGCCGGCAGGATCAAAAAAAAACTGGAATCACGTGGTAGATGCA
AGAGCAGGCCCTAGTCTAAAGACAACATTGAAACCAAAGAAAGTGAAAACTCTATCTGGAAACAGGATGAAAAGCAACCA
GATCAGCAAACTGCAGAAGGAATTTAAACGCCACAACTCTGATGCTCACAGTACCACCTCAAGTGCCTCTCCAGGCCAGT
CTCCATGCTACAGTAACCAGTCAGATGAGGGCTCAGATACAGAGATGGCTTCCAGCTCTAATAGAACTCCGGTTTTTTCC
TTCTTAGATCTTACCTACTGGAAAAGACAGAAAATATGTTGTGGGATCATCTATAAAGGCCGTTTTGGGGAAGTCCTCAT
CGACACTCATCTCTTCAAGCCTTGCTGCAGCAGTAAGAAAGCAGCTGCCGAGAAGCCCGAGGAGCAGGGGCCGGCACCTC
TGCCCATCTCCACTCAGGAGTGG

Alignment

ORF - retro_mmus_1234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGS
          MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAG.
Retrocopy MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGX

Parental  KKNWNHVVDARAGPSLKTTLKPKKVKTLSGNRMKSNQISKLQKEFKRHNSDAHSTTSSASPAQSPCYSNQ
          ...WNHVVDARAGPSLKTTLKPKKVKTLSGNRMKSNQISKLQKEFKRHNSDAHSTTSSASP.QSPCYSNQ
Retrocopy XXXWNHVVDARAGPSLKTTLKPKKVKTLSGNRMKSNQISKLQKEFKRHNSDAHSTTSSASPGQSPCYSNQ

Parental  SDEGSDTEMASSSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSSKKAAAEKPEEQG
          SDEGSDTEMASSSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSSKKAAAEKPEEQG
Retrocopy SDEGSDTEMASSSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSSKKAAAEKPEEQG

Parental  PAPLPISTQEW
          PAPLPISTQEW
Retrocopy PAPLPISTQEW

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	0.12 RPM
SRP007412_cerebellum	0.00 RPM	0.30 RPM
SRP007412_heart	0.00 RPM	0.28 RPM
SRP007412_kidney	0.00 RPM	1.06 RPM
SRP007412_liver	0.00 RPM	0.22 RPM
SRP007412_testis	0.00 RPM	0.73 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1234 was not detected

EST

3 EST(s) were mapped to retro_mmus_1234 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY077132	119278402	119278759	100	357	0	357
CD564436	119278449	119278632	99.5	182	1	181
CD564559	119278427	119278784	100	357	0	357

TSS

No TSS is located nearby retro_mmus_1234 retrocopy 5' end.

Lab

retro_mmus_1234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1234 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni	ENSCHOG00000007193	17 retrocopies	retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971, retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Mus musculus	ENSMUSG00000039985	4 retrocopies	retro_mmus_1234 , retro_mmus_1471, retro_mmus_1557, retro_mmus_3331,
Oryctolagus cuniculus	ENSOCUG00000008618	1 retrocopy	retro_ocun_1176,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,
Tursiops truncatus	ENSTTRG00000008465	3 retrocopies	retro_ttru_1162, retro_ttru_1498, retro_ttru_984,