RetrogeneDB ID: retro_mmus_164

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:46051814..46052294(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000069899
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Sft2d1
• Ensembl ID: ENSMUSG00000073468
• Aliases: Sft2d1, 5630401J11Rik, AA409698
• Description: SFT2 domain containing 1 [Source:MGI Symbol;Acc:MGI:1918689]

Sequence

>retro_mmus_164
ATGGAGAAGCTGCGGCGCGTCTTGAGCGGCCAGGACGACGAGGAGCAAGGCCTGACGGCGCAGGTCCTGGATGCCTCATC
CCTGAGTTTCAACACCAGGTTGAAGTGGTTTGTCATATGCTTTGTTGCTGGCATTTTCTTTTCATTCCTTGGAACAGGGT
TGCTATGGCTTCCCAATGGCATGAAACTCTTTGCAGTATTTTACACCCTTGGAAACCTTGCTGCATTGGCCAGTACATGC
TTTTTAATGGGACCTGTGAAGCAACTGAAGAAAATGTTTGAAACAACAAGATTGCTTGCAACAATTATTATGCTTTTGTG
CCTGGTATTTACCCTGTGTGCTGCTCTGTGGTGGCGGAAGAAGGGGCTGGCCTTACTCTTCTGCATATTGCAGTTCTTGT
CGATGACCTGGTACAGTCTGTCCTACATCCCGTATGCAAGGGACGCGGTGCTCAAGTGCTGCTCCTCACTCTTGGGTTGA

Alignment

ORF - retro_mmus_164 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  MEKLRRVLSGQDDEEQGLTAQVLDASSLSFNTRLKWFVICFVAGIFFSFLGTGLLWLPNGMKLFAVFYTL
          MEKLRRVLSGQDDEEQGLTAQVLDASSLSFNTRLKWFVICFVAGIFFSFLGTGLLWLPNGMKLFAVFYTL
Retrocopy MEKLRRVLSGQDDEEQGLTAQVLDASSLSFNTRLKWFVICFVAGIFFSFLGTGLLWLPNGMKLFAVFYTL

Parental  GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCLVFTLCAALWWRKKGLALLFCILQFLSMTWYSL
          GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCLVFTLCAALWWRKKGLALLFCILQFLSMTWYSL
Retrocopy GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCLVFTLCAALWWRKKGLALLFCILQFLSMTWYSL

Parental  SYIPYARDAVLKCCSSLLG
          SYIPYARDAVLKCCSSLLG
Retrocopy SYIPYARDAVLKCCSSLLG

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	0.21 RPM	13.15 RPM
SRP007412_cerebellum	0.09 RPM	13.68 RPM
SRP007412_heart	0.16 RPM	7.22 RPM
SRP007412_kidney	0.19 RPM	10.14 RPM
SRP007412_liver	0.16 RPM	8.60 RPM
SRP007412_testis	0.09 RPM	4.39 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_164 was not detected

EST

No EST(s) were mapped for retro_mmus_164 retrocopy.

TSS

No TSS is located nearby retro_mmus_164 retrocopy 5' end.

Lab

retro_mmus_164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164 ,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,