RetrogeneDB ID: retro_sscr_879

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:95379547..95380461(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSSSCG00000015473
• Aliases: None
• Description: transmembrane protein 183A [Source:HGNC Symbol;Acc:20173]

Sequence

>retro_sscr_879
AGTCTCTGTGGCTTGGAAGCCTCCCAGTTTCCTGCAGTAGAAGCTCTTTCTGGGGCTGGTGAGCCTTGTGACATCATTGA
CAGCAGCAATGAGATGGATGCCCAGGAGGAAAGCATGCATGAGAAAACTGTCTCCAGAAAAAAGAAAAGAAAGGGGCACA
AAGATGACTGGGACAGAGCTGGGGGAGAAGAGTATCCCATGGATATTTGGCTACTGCTGGCTTCCGATATCTTCCCAAGG
ACCTTGTGAATTGTTCCCTGATTTGTAAGGATGCCTGGACTTTCACTGGCACTGCTGCCTTTTGGACCAGGTTGTACCGC
AGGCACTACATGCCAGATGCCTCTCCGCCTTGGTGCCCCCAACCAGAGTCAATGGAGAAGCTGCACCGTCTCTGAGCACT
TGTGATCCGATCCATGTATGAGCCATTTGCTACATTCAAATCTCCAGAATCTAGCCATTCCAGAAAGCACTCCCAGCACT
TTCAAGAATGCCAAATCCTTACTTTTCTGGTACGAAAAGAGTGTAGAAACCAGACAGGAACCAATGCGGGAGTTCAAATT
CAAAAAAACAGTCCCCTTCAATTAAAGAGCAAGTATATATGGGAGGATTGCAGCCTCCTATGCAGTATGAAAATGTCCAC
GCCAACCCAGACCAGGACTGCTGCCCACTGTAGGTCACCACTCTCAAGTTCAACTCTATTCCAATTGTTATGGGAATGAT
AGTTACCCTGTTTGTTATCAGTGTGAGCCTGGACATGTGGCATCATCGAATGAGCCGGGTGTTCCCAAGATTCTCCTGAC
CATGGTAGTCAGAAACTGCGCGATGAACAGGTTATTCAAGACATCCTGGACCTGGGACACAGTGTTGGACTTTGCGACCA
GTGGCATCCTCAGAATCTGTTCTCTCTGAAAGCA

Alignment

ORF - retro_sscr_879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.29 %
• Parental protein coverage: 81.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLCGLEASQVPAVEALSGAGEPCDIIDSSDEIDAQEESIHERTVCRKKKSKRHKEDLDRAGGEEYPMDIW
          SLCGLEASQ.PAVEALSGAGEPCDIIDSS.E.DAQEES.HE.TV.RKKK.K.HK.D.DRAGGEEYPMDIW
Retrocopy SLCGLEASQFPAVEALSGAGEPCDIIDSSNEMDAQEESMHEKTVSRKKKRKGHKDDWDRAGGEEYPMDIW

Parental  -LLLAS-YIVLDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSL
          .LL....Y...D.VN.SLICK.AWT.T.TAAFWTRLYRRHY..DAS.P....PESMEKL..L.A.VIRS.
Retrocopy LLLASD<YLPKDLVNCSLICKDAWTFTGTAAFWTRLYRRHYMPDASPPWCPQPESMEKLHRL*ALVIRS-

Parental  YHMYEPFAARIS-KNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKK-QSPRLKSKC-MGG
          ..MYEPFA...S..N.AIPESTPST.KN.K.LLFW..K.V..RQEPM.EF..KFKK.QSP..K....MGG
Retrocopy --MYEPFATFKS>QNLAIPESTPSTFKNAKSLLFWYEKSVETRQEPMREF--KFKK>QSPSIKEQVYMGG

Parental  LQPPIQYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVF-QDSPVHGGRK
          LQPP.QYE.VH.NPDQDCC.L.VTTL.F..IPIVMGMI.TLF.I.VS.DM.HHR...VF.QDSP.HG..K
Retrocopy LQPPMQYENVHANPDQDCCPL*VTTLKFNSIPIVMGMIVTLFVISVSLDMWHHRMSRVF>QDSPDHGSQK

Parental  LRSEQGVQVILDPVHSVRLFDWWHPQYPFSLRA
          LR.EQ..Q.ILD..HSV.L.D.WHPQ..FSL.A
Retrocopy LRDEQVIQDILDLGHSVGLCDQWHPQNLFSLKA

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	21.77 RPM
SRP014902_testis	0.00 RPM	35.50 RPM
SRP018288_heart	0.00 RPM	34.05 RPM
SRP018288_kidney	0.10 RPM	46.10 RPM
SRP018288_liver	0.00 RPM	31.82 RPM
SRP018288_lung	0.00 RPM	32.79 RPM
SRP018856_adipose	0.05 RPM	28.40 RPM
SRP035408_brain	0.00 RPM	32.81 RPM
SRP035408_liver	0.00 RPM	24.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_879 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_879 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879 ,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,