RetrogeneDB ID: retro_mmus_2795

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:142110934..142111522(+)
• Located in intron of: ENSMUSG00000079262

Retrocopy information

• Ensembl ID: ENSMUSG00000092488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sord
• Ensembl ID: ENSMUSG00000027227
• Aliases: Sord, Sdh-1, Sdh1, Sodh-1
• Description: sorbitol dehydrogenase [Source:MGI Symbol;Acc:MGI:98266]

Sequence

>retro_mmus_2795
CTCTCTGTGGGGATCTATGCCTGCTGTCCAGGTTCAGTTTCCCTGGGAAATAAGGCCCTCGTGTGTGGAGCTGAGAGAGC
TGGGATAGTCATTTTGCTTGTGTCCAAAGCAGTTGGAGCTGCTCAAATGGTGGTGACTGAACTATCTGCTGCTTGGTTAA
CTAAAGCCAAGGATGTTGGGGCAGACTTTACCATCCAGGTTGCCAAAGAGACCCCTCAAGAAATTGCCAGTAAGGCGGAA
AGTCTGCTGGGGAGCAAGCCGGAGATCACCATTGAATGCACAGGAGCGCAGTCCTCCATCCAGATGTGCATCTGTGCCAC
TCACTCTGGTGGGACCTTGGTGATTGTGGGAATGGTGATGATCAATTTACTCCTAGTCCATGCAGCCATGCCGGAGGTGA
ATATCAAAGGCGTGTTTCGATACTGCAACCCGCGGCCGATTTCCATGCTTACATTGAAGACTTTGAATGTAAAACCCTTA
GTTACCCACAGATTCCCTCTGGAAAAGGATGGAGACGCCTTTGAAACAGCCAAAAAGGGAGTGGGGCTGAAAGTTACGAT
CAAGTGTGACCCCAATGACAAGAACCCC

Alignment

ORF - retro_mmus_2795 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79. %
• Parental protein coverage: 56.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSVGIYACRRGSVSLGNKVLVCGAGPVGMVTLLVAKAMGAAQVVVTDLSASRLTKAKEVGADFTIQVGKE
          LSVGIYAC..GSVSLGNK.LVCGA...G.V.LLV.KA.GAAQ.VVT.LSA..LTKAK.VGADFTIQV.KE
Retrocopy LSVGIYACCPGSVSLGNKALVCGAERAGIVILLVSKAVGAAQMVVTELSAAWLTKAKDVGADFTIQVAKE

Parental  TPQEIASKVESLLGSKPEVTIECTGAESSVQTGIYATHSGGTLVIVGMGAEMVNLPLVHAAIREVDIKGV
          TPQEIASK.ESLLGSKPE.TIECTGA.SS.Q..I.ATHSGGTLVIVGM...M.NL.LVHAA..EV.IKGV
Retrocopy TPQEIASKAESLLGSKPEITIECTGAQSSIQMCICATHSGGTLVIVGM--VMINLLLVHAAMPEVNIKGV

Parental  FRYCNTWPMAISMLASKTLNVKPLVTHRFPLEKAVEAFETAKKGVGLKVMIKCDPNDQNP
          FRYCN..P..ISML..KTLNVKPLVTHRFPLEK...AFETAKKGVGLKV.IKCDPND.NP
Retrocopy FRYCN--PRPISMLTLKTLNVKPLVTHRFPLEKDGDAFETAKKGVGLKVTIKCDPNDKNP

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	10.42 RPM
SRP007412_cerebellum	0.00 RPM	9.77 RPM
SRP007412_heart	0.00 RPM	83.68 RPM
SRP007412_kidney	0.46 RPM	478.53 RPM
SRP007412_liver	0.00 RPM	795.80 RPM
SRP007412_testis	0.14 RPM	491.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2795 was not detected

EST

No EST(s) were mapped for retro_mmus_2795 retrocopy.

TSS

No TSS is located nearby retro_mmus_2795 retrocopy 5' end.

Lab

retro_mmus_2795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2795 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025496	1 retrocopy	retro_btau_1805,
Ciona intestinalis	ENSCING00000021861	1 retrocopy	retro_cint_5,
Mustela putorius furo	ENSMPUG00000010850	1 retrocopy	retro_mputfur_201,
Mus musculus	ENSMUSG00000027227	2 retrocopies	retro_mmus_2795 , retro_mmus_505,
Rattus norvegicus	ENSRNOG00000017291	7 retrocopies	retro_rnor_1272, retro_rnor_1813, retro_rnor_2021, retro_rnor_2022, retro_rnor_2023, retro_rnor_2024, retro_rnor_2857,