RetrogeneDB ID: retro_sscr_233

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:78380586..78381799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAU1
• Ensembl ID: ENSSSCG00000027444
• Aliases: None
• Description: staufen double-stranded RNA binding protein 1 [Source:HGNC Symbol;Acc:11370]

Sequence

>retro_sscr_233
GTGAATGGAAGAGAATCAGAAGAAGAAAATCTCAAAAACCTGAAATCATTCAAGTATTTGATATTGCACTTAAATGTAAC
TTGCGAGTGAATTTTTAGGTTTCCCGGGAGAGTGGCCCACCCCACATGAACAGCTTTGTGACCAGGGTGTCAGTTTGGGG
AGTTTATAGTAGAAGGTGAAGGGAAGAGCAAGAATATTCCAAAGGAAAATGCTGGATAGCTGTTCTTGAGGAGCTGAAGA
AGTTACTGTCTCTGCCTATAGTTGAGCAAGTGAAGCCCAGAATCAAAAAGAAAACAGTCAATAATCTGGTTATAGAGCAC
TCAGGAATATGGGCAGGTGATGTATCCCATTAGCAGACTGGCCCAGATCCAGCAGGTGAAAAAGGAGAAGGAGTTATTGT
ACCTTCTTCCCACCAAGTGAGGCCTCCCAAGCTGCAGGGACTTTATGATGCAAGTAAAGGTGGGAAAAAAAACACTGCCA
AAGGATCTGGCACAAAGAAGAACATTACCAAACATAATGCAGCCAAGAGTATGCTGGAGATCCTTAGTTTCAAGGTCCCA
CAGACTCAGCCCACCAAACCAGCCCTCAAATATGAGGAGAGGACACACCAAAAACATCAAGGGATGGAAGAAAAGTAGCC
TTTTTTGAACCTGGTTCTGGGGATGAAAATGGTACTAGCAATTAAGAGGATGAGTCATTATTTTAGCCACATCTTAGTCA
TCAGCACCTGCTTGCTGGAATTCTTCCCAGGGTGCATGAGGTTGCCATGGCCATAGAGGTTATTCAAGGACATCACACCA
AGTATTTCACCAGGATAGCTCCAAAGCCTGCCAAGACCATGGTAACTGCCAAGATAGCCCATGAATTGTGTGGGGACAGC
TTGCCTGCAGCCAAGACCATTTTAAAGAACAACATCTCTTCAGGTCATATTCCCCATGGACTCCTCATGAGACCCTCTTA
GCAGTTGGACTACCTTTCCAGAGTCCAGGGATTCCAGGTTTAATACAAAGACTTCCCCAAAAGCACAAGAATTAATATAT
TATCTCTTATAAATTGTTCCTCTCAGCCACATCTGATCAGCCAGGGTACCAGAAACGATGTGTAGTCCTGCCATGACATG
GCTGCAATAAAAAATTTAAAGTTGCTTCCTGAGTTGGACCAACAAAATACAGAGATGCCAAGAACAGGAAATGGACCAAT
GTCTGTGTATGGG

Alignment

ORF - retro_sscr_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.7 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VNGRESEEENLN-KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTRVSV-GEFVGEGEGKSKKISK
          VNGRESEEENL..K.EI.QVF.IALK.NL.VNF.V.RESGPPHM.SFVTRVSV.GEF..EGEGKSK.I.K
Retrocopy VNGRESEEENLK<KPEIIQVFDIALKCNLRVNF*VSRESGPPHMNSFVTRVSV>GEFIVEGEGKSKNIPK

Parental  KNAA-IAVLEELKKLPPLPTVERVK-PRIKKKTKSIVRLQSTQEYGQGMNPISRLAQIQQAKKEKEPEYL
          .NA..IAVLEELKKL..LP.VE.VK.P..K.K..SI..L.STQEYGQ.M.PISRLAQIQQ.KKEKE..YL
Retrocopy ENAG<IAVLEELKKLLSLPIVEQVK>PESKRK-QSIIWL*STQEYGQVMYPISRLAQIQQVKKEKELLYL

Parental  LLTERGLPRRREFVMQVKV-GNHTAEGSGTNKK-VAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPI
          L.T..GLP..R.F.MQVKV.G..........KK...K.NAA..MLEIL.FKVPQ.QPTKPALK.EE.T..
Retrocopy LPTK*GLPSCRDFMMQVKV<GXXXTAKGSGTKKNITKHNAAKSMLEILSFKVPQTQPTKPALKYEERTHQ

Parental  KKPG-DGRKVTFFEPGSGDENGTSNKEDEFRM-PYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRV
          K..G.DGRKV.FFEPGSGDENGTSN.EDE....P.LSHQ.L.AGILP.V.EVA.A..V.QGHHTK.FTR.
Retrocopy KHQG<DGRKVAFFEPGSGDENGTSN*EDESLF*PHLSHQHLLAGILPRVHEVAMAIEVIQGHHTKYFTRI

Parental  APNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKN
          AP.PAK..VTA.IA.EL..G...P.A.TILKNNISSGH.PHG.L.RPS.QLDYLSRVQGFQV.YKDFPK.
Retrocopy APKPAKTMVTAKIAHELC-GDSLPAAKTILKNNISSGHIPHGLLMRPS*QLDYLSRVQGFQV*YKDFPKS

Parental  NKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQNTEMPRTGNGPMSVCG
          ......SLINCSSQP.LIS.G...DV.SCHDMAA...LKLL.ELDQQNTEMPRTGNGPMSV.G
Retrocopy TRINILSLINCSSQPHLISQGTRNDV*SCHDMAAIKNLKLLPELDQQNTEMPRTGNGPMSVYG

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	68.36 RPM
SRP014902_testis	0.00 RPM	98.16 RPM
SRP018288_heart	0.00 RPM	55.66 RPM
SRP018288_kidney	0.00 RPM	117.71 RPM
SRP018288_liver	0.00 RPM	87.31 RPM
SRP018288_lung	0.00 RPM	116.59 RPM
SRP018856_adipose	0.00 RPM	118.34 RPM
SRP035408_brain	0.00 RPM	68.60 RPM
SRP035408_liver	0.00 RPM	115.93 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_233 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_233 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016233	1 retrocopy	retro_cjac_4102,
Monodelphis domestica	ENSMODG00000016276	1 retrocopy	retro_mdom_1931,
Sus scrofa	ENSSSCG00000027444	1 retrocopy	retro_sscr_233 ,