RetrogeneDB ID: retro_sscr_327

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:109282162..109282651(+)
• Located in intron of: ENSSSCG00000022952

Retrocopy information

• Ensembl ID: ENSSSCG00000030593
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSSSCG00000001959
• Aliases: None
• Description: Sus scrofa cofilin 2 (muscle) (CFL2), mRNA. [Source:RefSeq mRNA;Acc:NM_001025215]

Sequence

>retro_sscr_327
ATGGCCTCTGGTATGGCTGTCTCTGACGGGGTCATCAAAGTGTTTAATGACATGAAGGTGCGTTAAGTCCTCGACACCAA
AGGAGGTGAAGAAGCGCAAGAAGGCGGTGCTCTTCTGCCTGAGCGAGGACAAGAACATCCTGGAGGGCAAGGAGATCCTC
GTGGGTGACATGGGCCAGACTGTAGACGACCCTATGCCACCTTTGTCAAGATGCTGCTGGACAAGGACTGCCGCTACGCC
CTCTATGACGCGACCCACGAGACCAAGGAGAGCCAGAAGGAGAACCTGGTGTTCATCTTGTGGGCCCCTGAGTGTGCACC
CCTGAAGAGCAAAATGATCTACGCCAGCTCCAAGGATGCCATCAAGAAGAAGCTGACAGGGATCAAGCATGAATTACAAG
CGAACTGCTACGAGCAGGTCAAGGACCGCCGCACCCTGGCAGAGAAGCTGGGGGGCAGCGCCGTCATCTCCCTGGAGAGC
AAGCCTTTG

Alignment

ORF - retro_sscr_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASGVTVNDEVIKVFNDMKVR-KSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDP-Y
          MASG..V.D.VIKVFNDMKVR.KSST..E.KKRKKAVLFCLS.DK......E.K.ILVGD.G.TV.DP.Y
Retrocopy MASGMAVSDGVIKVFNDMKVR>KSSTPKEVKKRKKAVLFCLSEDKN---ILEGKEILVGDMGQTVDDP<Y

Parental  TSFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVN
          ..FVK.L...DCRYALYDAT.ETKES.KE.LVFI.WAPE.APLKSKMIYASSKDAIKKK.TGIKHE.Q.N
Retrocopy ATFVKMLLDKDCRYALYDATHETKESQKENLVFILWAPECAPLKSKMIYASSKDAIKKKLTGIKHELQAN

Parental  GLDDIKDRSTLGEKLGGNVVVSLEGKPL
          .....KDR.TL.EKLGG..V.SLE.KPL
Retrocopy CYEQVKDRRTLAEKLGGSAVISLESKPL

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
SRP014902_placenta	157.95 RPM	1.86 RPM
SRP014902_testis	42.43 RPM	9.90 RPM
SRP018288_heart	6.99 RPM	687.11 RPM
SRP018288_kidney	43.34 RPM	50.43 RPM
SRP018288_liver	23.99 RPM	34.54 RPM
SRP018288_lung	182.98 RPM	52.13 RPM
SRP018856_adipose	30.19 RPM	27.90 RPM
SRP035408_brain	70.79 RPM	33.95 RPM
SRP035408_liver	18.02 RPM	20.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_327 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_327 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 37 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	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 ,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
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,