RetrogeneDB ID: retro_mmus_660

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:83478806..83479290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cfl2
• Ensembl ID: ENSMUSG00000062929
• Aliases: None
• Description: cofilin 2, muscle [Source:MGI Symbol;Acc:MGI:101763]

Sequence

>retro_mmus_660
ATGGCCTCAGGAGTTCAAGTTGAGGATGAAGTATGCCACATTTTCTACATTAAAGTTCAGAAATGTTCCACACCAGAAGA
AATCAAGAAAAGAAAGGCTATCATTTTCTGCCTCATTGCAGACAAAAAGTGTACAGTCGTTGAAGAAGGCAAAGAGATCT
TGGTGGCAGATGTTCCTGTTACCATAACTTATCCTCCTTTCAAGCATTTTGCCAGAAAGATTGCTCCCTTAAGAAGATTG
TTGCTACACTTTGTATGACACCAGCTTTGAAACCAAGGTGTACAGAAAAGAAGAGCTGATGTTCTTCTTGTGGGCTCCAG
AACAAGCACCTCTGAAAAGTAAAATGGTCTATGCAGGCTCGAAGGACACCATCAACAAGAAATTTCCAGGTATAAAGCAT
GAGTATCAAGCAAATGGACCAGAAGACCTCAATCAGACTAGTATTGCTGAAAGGCTAGGTGGCTCCTTAACTGTAGCTTT
TGAA

Alignment

ORF - retro_mmus_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.15 %
• Parental protein coverage: 97.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVE-DPYT
          MASGV.V.DEV...F...KV.K.ST.EEIKKRK.A..FCL..DK....VEE.K.ILV.D...T....P..
Retrocopy MASGVQVEDEVCHIFY-IKVQKCSTPEEIKKRK-AIIFCLIADKKCTVVEEGKEILVADVPVTITYPPFK

Parental  SFV-KLLPL-NDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQV
          .F..K..PL..DC.Y.LYD...ETK...KE.L.F..WAPE.APLKSKM.YA.SKD.I.KKF.GIKHE.Q.
Retrocopy HFARKIAPL>EDCCYTLYDTSFETKVYRKEELMFFLWAPEQAPLKSKMVYAGSKDTINKKFPGIKHEYQA

Parental  NGLDDIKDRSTLGEKLGGSVVVSLE
          NG..D........E.LGGS..V..E
Retrocopy NGPEDL-NQTSIAERLGGSLTVAFE

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	0.33 RPM	45.88 RPM
SRP007412_cerebellum	0.43 RPM	35.13 RPM
SRP007412_heart	0.12 RPM	128.41 RPM
SRP007412_kidney	0.10 RPM	65.49 RPM
SRP007412_liver	0.00 RPM	29.77 RPM
SRP007412_testis	0.09 RPM	50.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_660 was not detected

EST

No EST(s) were mapped for retro_mmus_660 retrocopy.

TSS

No TSS is located nearby retro_mmus_660 retrocopy 5' end.

Lab

retro_mmus_660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000032562	1 retrocopy	retro_cfam_1006,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus	ENSFCAG00000008480	2 retrocopies	retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Loxodonta africana	ENSLAFG00000010579	1 retrocopy	retro_lafr_1041,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus	ENSMICG00000009237	1 retrocopy	retro_mmur_493,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127, retro_mmus_3556, retro_mmus_719, retro_mmus_970,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660 ,
Otolemur garnettii	ENSOGAG00000032321	1 retrocopy	retro_ogar_2346,
Pteropus vampyrus	ENSPVAG00000002798	1 retrocopy	retro_pvam_398,
Rattus norvegicus	ENSRNOG00000045892	1 retrocopy	retro_rnor_684,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Sus scrofa	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
Ictidomys tridecemlineatus	ENSSTOG00000001675	3 retrocopies	retro_itri_1313, retro_itri_581, retro_itri_632,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,