RetrogeneDB ID: retro_mmus_1757

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:28187329..28188828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Csde1
• Ensembl ID: ENSMUSG00000068823
• Aliases: Csde1, AA960392, BC016898, D3Jfr1, mKIAA0885, unr
• Description: cold shock domain containing E1, RNA binding [Source:MGI Symbol;Acc:MGI:92356]

Sequence

>retro_mmus_1757
TCCCTACATCCTGGAGATGACGTGGAACTCACAATCAAGTACAGAAATGCTAAAGAAGTTGCAACAGATGTCAGACTATT
GCCTCAAGGAACAGTCATTTTTGAAGATATCAGCACTGAACATTTTGAAGGAACTATAACCAAAGATATCCCAAAAGTAC
CCAGTAAAAACCAGAATGACCCATAGCTAGGATGAATCAAAGTTGACTTTGTGAGTCCTAAAGAACTTCCCTTTGGAGAC
AAAGACACAAAATCCAAAGTGAACCTGCTGGAAGGTGACCATGTTAGCTTTAATATTTCAACAGACCGACGTGACAAATT
AGATCGAGCAACCAACATAGAGGTTCTATCAAATCCATTTCAGTTCACTAATGAAGCCAGAGAGATGGGTGTGATTGCTG
CTGTGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGACATTCTAGAC
GGGAACCAGCTCCACACTGCAGATGAAGCAGAGTTCACTGTGGTTCCTGTTATGCTCTCTGCCCAAAGAAATCATGCTGT
TAGGATTAAGAAACTTCCCAAGGGCACGGTTTTAGTCCCTTCCCATTCAGATTGTCGTTTTCTGGGCACCATAGAAAAAG
AAGCCACTTTTTTAAATCCTAAAACTACAAGCCCAAATAAAGACAAAGACAAGGAGGCAGAAGATGGCATTACAGCTTAT
GATGACTGTGGTGTGAAACTGACAATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTATTTCTCCTCAGATAGGAGAGAA
GGTTGATTTTAGGATTAGTGACAAACAGAGGCCTGGACAGATTGCAACTTTTGTGAGACTTGTAGGTCATAATTCTACCT
CCAAAAGGCTCTCGAGTTATGTGGCAACTCTGAAAGATAATTTTGGATTTATAGAAACAGCTAATCATGATAAGGAAATA
TTTTTCATTAGAGTGAGTTCTCTGGTGATGTTGATAGCCTGGAACTGGGAGACATGGTTGAATACAGCTTGTCCAAAGGC
AAAGGCAATAATGTCAGTGCTGAGAAAGTAAACAAACCTCACTCAGTAAATGGCATTACTGAGGAAGCTAATCCCACCAT
CTACTCTGGTAAAGTCATTCGCCCTCTGAGAGGTGTTGATCCAACACAGATTGAGTACCAAGGACTGACTGAGACTGTGA
AGGAGGGGGATATGAAAGGTGAAGTGTATCCTTTTGGCACAGTTGGGATGGCCAACAAAGGGGATTGCCTACAGAAAGGG
GAGAGTGTCAAGTTCCAGTTGTGTGTACTTGGCCAAAATGCACAAACTATGGCCTACAACATCACACCCCTTCGTAGGGC
TACTGTGGAGTGTGTGAAAGATCAGTTTGGCTTTATTAACTATGAAATAAGAGATAGCAAGAAGCTCTTTTTCCATGTGA
AAGAAGTTCAGGATGGCGTTGAGCTACAGGCAGGAGATGAGGTGGAATTCTCAGTGATC

Alignment

ORF - retro_mmus_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.64 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLQPGDDVEFTIKDRNGKEVATDVRLLPQGTVIFEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDF
          .L.PGDDVE.TIK.RN.KEVATDVRLLPQGTVIFEDIS.EHFEGT.TK.IPKVPSKNQNDP..G.IKVDF
Retrocopy SLHPGDDVELTIKYRNAKEVATDVRLLPQGTVIFEDISTEHFEGTITKDIPKVPSKNQNDP*LG*IKVDF

Parental  VIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFG
          V.PKELPFGDKDTKSKV.LLEGDHV.FNISTDRRDKL.RATNIEVLSN.FQFTNEAREMGVIAA.RDGFG
Retrocopy VSPKELPFGDKDTKSKVNLLEGDHVSFNISTDRRDKLDRATNIEVLSNPFQFTNEAREMGVIAAVRDGFG

Parental  FIKCVDRDARMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGT
          FIKCVDRDARMFFHFS.ILDGNQLH.ADE.EFTVVP.MLSAQRNHA.RIKKLPKGTV...SHSD.RFLGT
Retrocopy FIKCVDRDARMFFHFSDILDGNQLHTADEAEFTVVPVMLSAQRNHAVRIKKLPKGTVLVPSHSDCRFLGT

Parental  VEKEATFSNPKTTSPNKGKDKEAEDGIIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQ
          .EKEATF.NPKTTSPNK.KDKEAEDGI.AYDDCGVKLTIAFQAKDVEGS.SPQIG.KV.F.ISDKQRPG.
Retrocopy IEKEATFLNPKTTSPNKDKDKEAEDGITAYDDCGVKLTIAFQAKDVEGSISPQIGEKVDFRISDKQRPG-

Parental  QIATCVRLLGRNSNSKRLLGYVATLKDNFGFIETANHDKEIF-FHYSEFSGDVDSLELGDMVEYSLSKGK
          QIAT.VRL.G.NS.SKRL..YVATLKDNFGFIETANHDKEIF.FH.SEFSGDVDSLELGDMVEYSLSKGK
Retrocopy QIATFVRLVGHNSTSKRLSSYVATLKDNFGFIETANHDKEIF<FH*SEFSGDVDSLELGDMVEYSLSKGK

Parental  GNKVSAEKVNKAHSVNGITEEANPTIYSGKVIRPLRGVDPTQIEYQGMIEIVEEGDMKGEVYPFGIVGMA
          GN.VSAEKVNK.HSVNGITEEANPTIYSGKVIRPLRGVDPTQIEYQG..E.V.EGDMKGEVYPFG.VGMA
Retrocopy GNNVSAEKVNKPHSVNGITEEANPTIYSGKVIRPLRGVDPTQIEYQGLTETVKEGDMKGEVYPFGTVGMA

Parental  NKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGVE
          NKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYE..DSKKLFFHVKEVQDGVE
Retrocopy NKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEIRDSKKLFFHVKEVQDGVE

Parental  LQAGDEVEFSVI
          LQAGDEVEFSVI
Retrocopy LQAGDEVEFSVI

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	0.02 RPM	218.63 RPM
SRP007412_cerebellum	0.09 RPM	220.62 RPM
SRP007412_heart	0.28 RPM	590.32 RPM
SRP007412_kidney	0.29 RPM	378.16 RPM
SRP007412_liver	0.11 RPM	228.52 RPM
SRP007412_testis	0.37 RPM	556.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1757 was not detected

EST

No EST(s) were mapped for retro_mmus_1757 retrocopy.

TSS

No TSS is located nearby retro_mmus_1757 retrocopy 5' end.

Lab

retro_mmus_1757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1757 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017129	1 retrocopy	retro_amel_1392,
Cavia porcellus	ENSCPOG00000000538	2 retrocopies	retro_cpor_1402, retro_cpor_513,
Myotis lucifugus	ENSMLUG00000005681	1 retrocopy	retro_mluc_1011,
Mus musculus	ENSMUSG00000068823	1 retrocopy	retro_mmus_1757 ,
Rattus norvegicus	ENSRNOG00000030302	1 retrocopy	retro_rnor_1429,