RetrogeneDB ID: retro_mmus_51

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:85098075..85098915(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000050035
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fhl1
• Ensembl ID: ENSMUSG00000023092
• Aliases: Fhl1, FHL-1, KyoT, RAM14-1, SLIM, SLIM-1
• Description: four and a half LIM domains 1 [Source:MGI Symbol;Acc:MGI:1298387]

Sequence

>retro_mmus_51
ATGTCTGAGTTCAAATGCCACCATTGCGAGGAATCCTTGCAAGGTAAAAAGTATGTGCAGAAGGATGGAGCCAACTACTG
TGTGACATGCTTTGACTCGCATTGTGCCAATATCTGTCAGGAATGCCACAAGCCCATAGGTGCAGATTCCAAGGAGGTGT
GTTATAAGGAGCAATTCTGGCACAACACCTGCTTCAAATGTTCCAAGTGTTCTCAACTCTTGGCTACTGAGACCTTTGTT
GCCTGGGACAAGAATATCCTGTGCAACAAGTGTGCCACTCGAGTCACCTTCCCCAAGTGCAAAGGGTGCCTCAAAGATAT
TGAGGAAGGAGACCATAATGTGGAATACAAAGGTAGTATCTGGCATAAAAACTGCTTTGTCTGCACCAACTGCAAGGACA
TCATTGGAACCAAAAATTTCTTCCCTAAAGATGAGGGATTCTACTGTGTGACTTGTTATGATGCCTTGTTTACCAAGCAT
TGTATGAAATGCAAAAAGCCCATCACATCTGGAGGAGTCAGTTACCAGGATCAGCCCTGGCATAGTGAGTGCTTTGTATG
TGTTTCCTGCTCTAAGGAGCTGAGTGGACAGCGTTTCACTGCTATGGATGACCAGTATTTTTGTGTGGATTGCTACAAGA
ACTATATAGCCAAGAAGTGTGCTGGGTGCAAGAACCCCATCACTGGGTTTGGTAAAGGCGCCAATGTGGTGGCCCATGAG
CAGAATTCCTGGCATGACTACTGCTTCAACTGCAAAACCTGTTCTGTAAATCTAGCCAATAAGCACTTTGTGTTTCATGA
TGAGCAGGTGTACTGTCCTGACTGTGCCAGAAATCTATAA

Alignment

ORF - retro_mmus_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 98.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFDCHYCRDPLQGKKYVQKDGRHCCLKCFDKFCANTCVDCRKPISADAKEVHYKNRYWHDNCFRCAKCLH
          .F.CH.C...LQGKKYVQKDG...C..CFD..CAN.C..C.KPI.AD.KEV.YK...WH..CF.C.KC..
Retrocopy EFKCHHCEESLQGKKYVQKDGANYCVTCFDSHCANICQECHKPIGADSKEVCYKEQFWHNTCFKCSKCSQ

Parental  PLASETFVSKDGKILCNKCATREDSPRCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFP
          .LA.ETFV..D..ILCNKCATR...P.CKGC.K.I..GD.NVEYKG..WHK.CF.C.NCK..IGT..FFP
Retrocopy LLATETFVAWDKNILCNKCATRVTFPKCKGCLKDIEEGDHNVEYKGSIWHKNCFVCTNCKDIIGTKNFFP

Parental  KGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHAECFVCVTCSKKLAGQRFTAVEDQYYCVDCY
          K.E.FYCVTC....F.KHC.KC.K.ITSGG..YQDQPWH.ECFVCV.CSK.L.GQRFTA..DQY.CVDCY
Retrocopy KDEGFYCVTCYDALFTKHCMKCKKPITSGGVSYQDQPWHSECFVCVSCSKELSGQRFTAMDDQYFCVDCY

Parental  KNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHNEQVYCPDCAKKL
          KN..AKKCAGCKNPITGFGKG..VVA.E..SWHDYCF.CK.CSVNLANK.FVFH.EQVYCPDCA..L
Retrocopy KNYIAKKCAGCKNPITGFGKGANVVAHEQNSWHDYCFNCKTCSVNLANKHFVFHDEQVYCPDCARNL

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	0.58 RPM	93.85 RPM
SRP007412_cerebellum	0.13 RPM	83.54 RPM
SRP007412_heart	0.09 RPM	86.45 RPM
SRP007412_kidney	0.06 RPM	138.08 RPM
SRP007412_liver	0.33 RPM	4.26 RPM
SRP007412_testis	1068.97 RPM	8.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_51 was not detected

EST

No EST(s) were mapped for retro_mmus_51 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_6685	1043 libraries	24 libraries	2 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_51 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_51 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_51 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51 ,
Nomascus leucogenys	ENSNLEG00000002560	1 retrocopy	retro_nleu_618,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,
Rattus norvegicus	ENSRNOG00000000875	1 retrocopy	retro_rnor_2514,