RetrogeneDB ID: retro_sscr_49

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:92721720..92722467(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031033
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSSSCG00000015317
• Aliases: None
• Description: family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]

Sequence

>retro_sscr_49
ATGGGGAAGCGGGATAATCGTGTAGCTTATATGAATCCTATAGCAATGGCCAGATGGCGGGGCCCCTCGCAATCTGCAGG
CCCAACAATACAAGATTATCTGAATCGACCGAGGCCGACCTGGGAAGAAGTGAAGAAACAATTAGAAAATAAAAAGAAAG
GCTCCAAGGCATTAGCTGAATTTGAAGAAAAAATGAATGAGAATTGGAAGAAAGAACTAGAAAAAAGCAGAGAGAAGTTA
TTAAGTGGAAACGAGAGCTCATCCAAGAAAAGGGAAAGAAAGAAAAAGAAAAAGAAGAAATCTTGTCAGTCTTCGTCGTC
TTCTTCATCAAGCTCTGATTCTTCAAGCAGTTCTTCAGATTCTGAGGATGAGGAGAAGAAACAAGGAAAAAAGAGAAAGA
AAAAAAAGAACCGTGCATACAAATCATCAGAAAGCTCTACATGTGAATCTGAATCAGAGAGCAAGGAATCTGTAAAAAAG
AAGAAGTCAAAGGATGAAACAGAGAAAGAAAAGTATATTAAAAGTCTCAGCAAAAAAAGAAAGAAGACTTATCCTGAAGA
TAAACCTTTATCATCAGAGCTCTCATCAGAATCAGATTATGAAGAGGAGATGCAAGCAAAGAAGAAAAGGAAACGTGACG
ATCGAGAAAAAGCAACAGAAAAAGCAAAGAAGAAGAAGAAGAAACAGCACAAAAAACATAGTAAGAAGAAGAAAAAGAAG
TCAGGTTCAAGTCACAAGTCAGGATAA

Alignment

ORF - retro_sscr_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 73.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENWKKELEKHREKLLSGSESSSKKRQRKKKEKKKSVFERLRKRKNSCISQASIVLCLVKYSSSSSSSS--
          E..KK.LE..........E...K.....KKE..KS....L.....S............K...SSSSSS..
Retrocopy EEVKKQLENKKKGSKALAEFEEKMNENWKKELEKSREKLLSGNESSSKKRERKKKKKKKSCQSSSSSSSS

Parental  -DSSSSSSDSEDEDKKQGKRKKKKKSRSHKSSESSMSETESDNKDSLKKKKKSKDITEKEKDVKGLSKKR
          .DSSSSSSDSEDE.KKQGK..KKKK.R..KSSESS..E.ES..K.S..KKKKSKD.TEKEK..K.LSKKR
Retrocopy SDSSSSSSDSEDEEKKQGKKRKKKKNRAYKSSESSTCESESESKESV-KKKKSKDETEKEKYIKSLSKKR

Parental  -KMYPEDKPLSSESLSESDYTEEVRAKKKKSSEEREKTTTSESQEKTKKKKKHKKHSKKKKKKAASS
          .K.YPEDKPLSSE..SESDY.EE..AKKK.....REK.T......K.KKKK.HKKHSKKKKKK..SS
Retrocopy KKTYPEDKPLSSELSSESDYEEEMQAKKKRKRDDREKAT---EKAKKKKKKQHKKHSKKKKKKSGSS

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	2.12 RPM
SRP014902_testis	0.85 RPM	10.75 RPM
SRP018288_heart	0.16 RPM	13.15 RPM
SRP018288_kidney	0.49 RPM	26.10 RPM
SRP018288_liver	0.00 RPM	18.07 RPM
SRP018288_lung	1.43 RPM	18.74 RPM
SRP018856_adipose	0.40 RPM	9.03 RPM
SRP035408_brain	47.99 RPM	129.39 RPM
SRP035408_liver	0.26 RPM	29.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_49 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_49 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_49 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_95
Macaca mulatta	retro_mmul_226

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49 ,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,