RetrogeneDB ID: retro_sscr_899

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:35490058..35490421(+)
• Located in intron of: ENSSSCG00000001532

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC42
• Ensembl ID: ENSSSCG00000003520
• Aliases: None
• Description: Sus scrofa cell division cycle 42 (GTP binding protein, 25kDa) (CDC42), mRNA. [Source:RefSeq mRNA;Acc:NM_001078680]

Sequence

>retro_sscr_899
ATGTAGACAATTAAGTGTGTTGTGGGCGATAGTGCCGTTGGTAAAACATGTCTCCTGATATCCTACACAACAAACAGATT
TCCATCTGTACCAACTGTTTTGGACAACTCTGCAGTCACAGTTATGATTGGTGAAGAGCCATACACTCTTGGACTTTTTG
ATACTGTAGGGCAAGAGGATTATGACAGATTACGACTGCTGAGTTATCCACAAACAGATGTATTTCTAGTCTGTTTTTCA
GTGGTCTCTCTATCCTTGTTTGAAAATGTGAAAGAAAAGTGGGTGCCGGAGATAACTCACCACTGTCCAAAGACTCCTTT
CTTGCTTATTGGGACCCAAATTGATCTCAGAGATGACCCCTCT

Alignment

ORF - retro_sscr_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 64.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPL
          M.TIKCVV.GD.AVGKTCLLISYTTN.FPS..VPTV.DN.AVTVMIG.EPYTLGLFDT.GQEDYDRLR.L
Retrocopy M*TIKCVV-GDSAVGKTCLLISYTTNRFPS--VPTVLDNSAVTVMIGEEPYTLGLFDTVGQEDYDRLRLL

Parental  SYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPS
          SYPQTDVFLVCFSVVS.S.FENVKEKWVPEITHHCPKTPFLL.GTQIDLRDDPS
Retrocopy SYPQTDVFLVCFSVVSLSLFENVKEKWVPEITHHCPKTPFLLIGTQIDLRDDPS

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	92.12 RPM
SRP014902_testis	0.00 RPM	102.12 RPM
SRP018288_heart	0.00 RPM	121.17 RPM
SRP018288_kidney	0.20 RPM	202.63 RPM
SRP018288_liver	0.16 RPM	97.07 RPM
SRP018288_lung	0.00 RPM	391.32 RPM
SRP018856_adipose	0.00 RPM	184.22 RPM
SRP035408_brain	0.00 RPM	271.27 RPM
SRP035408_liver	0.03 RPM	83.05 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_899 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus	ENSECAG00000019180	1 retrocopy	retro_ecab_11,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Homo sapiens	ENSG00000070831	6 retrocopies	retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Myotis lucifugus	ENSMLUG00000013365	4 retrocopies	retro_mluc_1076, retro_mluc_1864, retro_mluc_2456, retro_mluc_905,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,
Sus scrofa	ENSSSCG00000003520	1 retrocopy	retro_sscr_899 ,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Sus scrofa	ENSSSCG00000021944	4 retrocopies	retro_sscr_40, retro_sscr_565, retro_sscr_582, retro_sscr_882,