RetrogeneDB ID: retro_sscr_1198

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:65871856..65872313(-)
• Located in intron of: None

Retrocopy information

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

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_1198
ATGGCCTCCAGTATGACTGTCTCTGATGGGGTCTTCAAAGTGTTCACTGACATAAAAGTGCCTGAGTCTTTGACACCAGA
GGAAGTGAAGGAATGCAAGAAGGGGGTGCTCTTCTGCCTGAGCAAGGACAAGAACATCATCCTGAAGGAAGGCATGGAGA
TCCTGGTACATGATGTGGGCCAGTCTGTGGACGACCCTTAATGCCACCTTTGTCAAGATGCTGCCAGGCTAGGACTGCCA
CTAAGCCCTCTATGACACAAACTATGAGACTAAGGAGGGCAAGAAGGAGGACCTAGTGTTCATCTTCTGGGCTCCTGAGT
CTGCATCCCTTAAGAGCAAAATGATCTACGCCAGCTCCAAGGACACCATCAAGAAGGTAACAGGAGTCAAGGATAAATTA
GAAGCAAACTGCTATGAGGAGGTCGAGGACTGCTGCACTCTGGCAGAAAAGTTGGGT

Alignment

ORF - retro_sscr_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDP-YT
          MAS..TV.D.V.KVF.D.KV..S.T.EE.K..KK.VLFCLS.DK..II..E...ILV.D.G..V.DP...
Retrocopy MASSMTVSDGVFKVFTDIKVPESLTPEEVKECKKGVLFCLSKDKN-IILKEGMEILVHDVGQSVDDP>NA

Parental  SFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNG
          .FVK.LP..DC..ALYD..YETKE.KKEDLVFIFWAPESA.LKSKMIYASSKD.I.KK.TG.K.....N.
Retrocopy TFVKMLPG*DCH*ALYDTNYETKEGKKEDLVFIFWAPESASLKSKMIYASSKDTI-KKVTGVKDKLEANC

Parental  LDDIKDRSTLGEKLG
          .....D..TL.EKLG
Retrocopy YEEVEDCCTLAEKLG

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	0.00 RPM	1.86 RPM
SRP014902_testis	0.00 RPM	9.90 RPM
SRP018288_heart	0.00 RPM	687.11 RPM
SRP018288_kidney	0.00 RPM	50.43 RPM
SRP018288_liver	0.00 RPM	34.54 RPM
SRP018288_lung	0.00 RPM	52.13 RPM
SRP018856_adipose	0.00 RPM	27.90 RPM
SRP035408_brain	0.00 RPM	33.95 RPM
SRP035408_liver	0.00 RPM	20.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1198 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1198 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,