RetrogeneDB ID: retro_mmus_1657

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:66227247..66227792(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pphln1
• Ensembl ID: ENSMUSG00000036167
• Aliases: Pphln1, CR, HSPC206, HSPC232
• Description: periphilin 1 [Source:MGI Symbol;Acc:MGI:1917029]

Sequence

>retro_mmus_1657
TCTCACAGAGGAGATGAACCTGGCTACAGATGAAGAAGAGATGATCATTCCACAAGCTGGCAGCCTGACTACAGGGACAT
GAGAGATGACTTTAGAAGAAAGAGGTTTTACTCTTCCCATCATTCAAGAGATGGGTCCCCCCCATAAAAGGGACGCTCCC
TTCTTCAGAGAATCCCCCGTAGGCCGGAAGGACTCACCACACAGCAGATCCGGCACCAGTGTCAGCAGCAGAAGCTGTTC
TCCGGAGCGAAGCAGGACACACTCCTTCCACCCGTAGTAAAGAAGAGGTAAAGAGAGGTCCATCCAGTCTTTAAAAAACG
TCAAGAGATACTTCACCCTGAAGTTCATCAGCAGTTTCTTCATCCAAGATGCTAGACAAACCCAGCAGGCTAACTGAGAA
GGAACTTGCTGAGGCTGAAAGCAAGTGGGCTAACGAAACACTAGAGAATTCAGATGAAAATAACTTGGCTGAAATGTCTG
AGTTTGAGGCGGGGTCCGCGGCACCCTTATTTATTGACCAGACAGAAGAACCCGAGTCAAACACA

Alignment

ORF - retro_mmus_1657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.7 %
• Parental protein coverage: 61.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHPSDESGYRWLRDDHSTSRQPDYRDMRDGFRRKSFYSSHYSRDRSP-HKRDAPFFRESPVGRKDSPHSR
          SH..DE.GYR..RDDHSTS.QPDYRDMRD.FRRK.FYSSH.SRD.SP.HKRDAPFFRESPVGRKDSPHSR
Retrocopy SHRGDEPGYR*RRDDHSTSWQPDYRDMRDDFRRKRFYSSHHSRDGSP>HKRDAPFFRESPVGRKDSPHSR

Parental  SGSSVSSRSYSPERSRTHSFHQSQHRSKERSIQSVK-TSRDASPSSSSAVASSKALDKPSRLTEKELAEA
          SG.SVSSRS.SPERSRTHSFH....R.KERSIQS.K.TSRD.SP.SSSAV.SSK.LDKPSRLTEKELAEA
Retrocopy SGTSVSSRSCSPERSRTHSFHP**RRGKERSIQSLK>TSRDTSP*SSSAVSSSKMLDKPSRLTEKELAEA

Parental  ESKWANETLEKSDESNLAEMNEFEAGSTAPLFIDQTEEPESNT
          ESKWANETLE.SDE.NLAEM.EFEAGS.APLFIDQTEEPESNT
Retrocopy ESKWANETLENSDENNLAEMSEFEAGSAAPLFIDQTEEPESNT

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	0.56 RPM	30.37 RPM
SRP007412_cerebellum	1.13 RPM	25.23 RPM
SRP007412_heart	0.00 RPM	15.60 RPM
SRP007412_kidney	0.00 RPM	21.46 RPM
SRP007412_liver	0.00 RPM	12.23 RPM
SRP007412_testis	1.05 RPM	52.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1657 was not detected

EST

No EST(s) were mapped for retro_mmus_1657 retrocopy.

TSS

No TSS is located nearby retro_mmus_1657 retrocopy 5' end.

Lab

retro_mmus_1657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1657 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657 , retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,