RetrogeneDB ID: retro_sscr_635

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:117871447..117871846(+)
• Located in intron of: ENSSSCG00000014190

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX1
• Ensembl ID: ENSSSCG00000017529
• Aliases: None
• Description: chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]

Sequence

>retro_sscr_635
AAAAGGGGGGGGGAAGAGGTGCTAGAAGAAGAGAGAGAAGAATATGTGGTATAACAAGTTCTCAACATTCAAATGGTAAA
GGGCAAAGCGGAGTACCTCCTCAAGTGGAAGGGGTTCTCAGATGAGGACAACACATGGGAGCCAGAAGAGAACCTGGATT
GCCCCGACCTCATTGCTGAGTTTCTGCAGTCGCAGAAAACAGCCCATGAGACAGATAAATCAGAGGGAGGTAAGAGCAAA
GCTGATTCTGATTCAGTACATAAAGGGGAGGAGAGCAAACCAAAGAAGAAGAAAGAGCCAGAAAAGCCATGAGGCTTTGC
CCAGAGGTTGGAGCCAGGGCGGATTATTAGAGCTACAGACTCCAGTGGAGAACTCATGTTCCTGATGAAATGGAAAAAC

Alignment

ORF - retro_sscr_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.58 %
• Parental protein coverage: 72.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKTAHE
          K....EVLEEE.EEYVV..VL....VKGK.EYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKTAHE
Retrocopy KXXXXEVLEEEREEYVV*QVLNIQMVKGKAEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKTAHE

Parental  TDKSEGGKRKADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMKWKN
          TDKSEGGK.KADSDS..KGEESKPKKKK.E.EKP.GFA..LEP.RII.ATDSSGELMFLMKWKN
Retrocopy TDKSEGGKSKADSDSVHKGEESKPKKKK-EPEKP*GFAQRLEPGRIIRATDSSGELMFLMKWKN

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	12.34 RPM
SRP014902_testis	0.00 RPM	71.43 RPM
SRP018288_heart	0.00 RPM	42.88 RPM
SRP018288_kidney	0.00 RPM	61.86 RPM
SRP018288_liver	0.00 RPM	34.70 RPM
SRP018288_lung	0.81 RPM	41.65 RPM
SRP018856_adipose	0.00 RPM	69.62 RPM
SRP035408_brain	0.00 RPM	141.37 RPM
SRP035408_liver	0.00 RPM	45.33 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_635 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004890	2 retrocopies	retro_amel_1228, retro_amel_54,
Canis familiaris	ENSCAFG00000016832	1 retrocopy	retro_cfam_804,
Choloepus hoffmanni	ENSCHOG00000011957	2 retrocopies	retro_chof_1860, retro_chof_2185,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Homo sapiens	ENSG00000108468	3 retrocopies	retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Gorilla gorilla	ENSGGOG00000024063	3 retrocopies	retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Microcebus murinus	ENSMICG00000009510	4 retrocopies	retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Mustela putorius furo	ENSMPUG00000015302	1 retrocopy	retro_mputfur_1457,
Nomascus leucogenys	ENSNLEG00000002435	4 retrocopies	retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Oryctolagus cuniculus	ENSOCUG00000008021	3 retrocopies	retro_ocun_177, retro_ocun_442, retro_ocun_55,
Procavia capensis	ENSPCAG00000002381	2 retrocopies	retro_pcap_134, retro_pcap_308,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Sarcophilus harrisii	ENSSHAG00000008192	1 retrocopy	retro_shar_76,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Sus scrofa	ENSSSCG00000017529	1 retrocopy	retro_sscr_635 ,
Tupaia belangeri	ENSTBEG00000014931	39 retrocopies	retro_tbel_1388, retro_tbel_1557, retro_tbel_1613, retro_tbel_1655, retro_tbel_1663, retro_tbel_1794, retro_tbel_2124, retro_tbel_2130, retro_tbel_2281, retro_tbel_2313, retro_tbel_2346, retro_tbel_2539, retro_tbel_2559, retro_tbel_2571, retro_tbel_2587, retro_tbel_270, retro_tbel_2713, retro_tbel_2716, retro_tbel_2752, retro_tbel_2809, retro_tbel_2835, retro_tbel_2854, retro_tbel_2926, retro_tbel_2993, retro_tbel_303, retro_tbel_3236, retro_tbel_3370, retro_tbel_3685, retro_tbel_3998, retro_tbel_4032, retro_tbel_4202, retro_tbel_4611, retro_tbel_4630, retro_tbel_484, retro_tbel_558, retro_tbel_687, retro_tbel_792, retro_tbel_793, retro_tbel_938,