RetrogeneDB ID: retro_mmus_1460

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:38483700..38484412(+)
• Located in intron of: ENSMUSG00000075122

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ckb
• Ensembl ID: ENSMUSG00000001270
• Aliases: Ckb, B-CK, Bck, Ck-3, Ck3, Ckbb
• Description: creatine kinase, brain [Source:MGI Symbol;Acc:MGI:88407]

Sequence

>retro_mmus_1460
TACTGCAGCCGCGGGGAGCGCCGCGCCATCGAGAAGCTGGCAGTAGAAGCTCTGTCCAGCCTAGATGGCGACCTGTCTGG
CAGGTTCTATGCGATCAAGAGCATGACCGAGGCGGAGCAGCAGCAGCTCATTGACGACCACTTCCTCTTCGACAAGCCTG
TGTCGCCTCTGTTGCTGGCCTCCAGCATGGCCCGCGACTGGCCGGATGCTTGCTGGCATATGGCACAATGACAATAAGAC
TTTCCTGGTGTGGATCAACGAGGAGGACCACCTGCGGGTCATCTCCATGAAGAAGGGGGGCAACATGAAGGAAGTGTTCA
CCCGATTCTGCACCGGCCTCACTCAAATCGAAACTCTCTTCAAGTCCAAGAACTATGAGTTCATGTGGAGCCCTCACCTG
GGCTACATCCTCACACGCCCTTCCAACCTGGGCACCGGACTGCGGGCAGGTGTGCACATCAAGCTGCCCCACCTGGGGAA
GCACGAGAAGTTCTCGGAGGTGCTCAATCGGCTGCGGCTTCAGAAGCGAGGCACAGGTGGCGTGGACTCCGCTGCTGTCT
GTGGCGTGTTTGATGTCTCCAATGCTGACCGCCTGAGCTTCTCGGAGGTGGAGCTGGTGCAGATGGTGGTGGACGGAGTG
AAACTGCTCATTGAGATGGAGCAGCGGCTCGAGCAGGGTCAGGCAATCGACGACCTCATGCCGGCCCAGAAG

Alignment

ORF - retro_mmus_1460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HCSRGERRAIEKLAVEALSSLDGDLSGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDA
          .CSRGERRAIEKLAVEALSSLDGDLSGR.YA.KSMTEAEQQQLIDDHFLFDKPVSPLLLAS.MARDWPDA
Retrocopy YCSRGERRAIEKLAVEALSSLDGDLSGRFYAIKSMTEAEQQQLIDDHFLFDKPVSPLLLASSMARDWPDA

Parental  -RGIWHNDNKTFLVWINEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWNPHLGYILTC
          ..GIWHNDNKTFLVWINEEDHLRVISM.KGGNMKEVFTRFCTGLTQIETLFKSKNYEFMW.PHLGYILT.
Retrocopy >AGIWHNDNKTFLVWINEEDHLRVISMKKGGNMKEVFTRFCTGLTQIETLFKSKNYEFMWSPHLGYILTR

Parental  PSNLGTGLRAGVHIKLPHLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMV
          PSNLGTGLRAGVHIKLPHLGKHEKFSEVL.RLRLQKRGTGGVD.AAV.GVFDVSNADRL.FSEVELVQMV
Retrocopy PSNLGTGLRAGVHIKLPHLGKHEKFSEVLNRLRLQKRGTGGVDSAAVCGVFDVSNADRLSFSEVELVQMV

Parental  VDGVKLLIEMEQRLEQGQAIDDLMPAQK
          VDGVKLLIEMEQRLEQGQAIDDLMPAQK
Retrocopy VDGVKLLIEMEQRLEQGQAIDDLMPAQK

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	0.26 RPM	643.25 RPM
SRP007412_cerebellum	0.04 RPM	739.20 RPM
SRP007412_heart	0.03 RPM	39.54 RPM
SRP007412_kidney	0.02 RPM	47.07 RPM
SRP007412_liver	0.00 RPM	3.71 RPM
SRP007412_testis	0.00 RPM	3.61 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1460 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	16:38479683..38483618

EST

No EST(s) were mapped for retro_mmus_1460 retrocopy.

TSS

No TSS is located nearby retro_mmus_1460 retrocopy 5' end.

Lab

retro_mmus_1460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1460 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460 , retro_mmus_1578, retro_mmus_1647, retro_mmus_2390,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,