RetrogeneDB ID: retro_sscr_70

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:66478980..66480225(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000010203
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSSSCG00000014022
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]

Sequence

>retro_sscr_70
ATGATGTTGGGCCCTGAGGGAGGTGAAGGTTTTGTGGTCAAGCTCCGTGGCCTGCCCTGGTCCTGCTCTGTTGAGGATGT
GCAGAATTTCCTCTCCGACTGCACAATTCGTGATGGGGCCGCAGGTGTTCATTTTATCTACACTAGAGAAGGCAGGCAGA
GTGGTGAGGCTTTTGTTGAACTTGAATCAGAAGATGATGTAAAAATGGCCCTTAAAAAAGACAGGGAAAGCATGGGACAC
CGGTACATTGAGGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGTGGTCCAAATAGTGCAGACAC
TGCCAATGATGGTTTCGTGCGGCTTCGAGGACTCCCATTTGGATGCACCAAGGAAGAAATCGTTCAGTTCTTCTCAGGGT
TGGAAATCGTGCCAAATGGGATCACACTGCCTGTGGACCCCGAGGGCAAGATTACAGGGGAAGCCTTTGTGCAGTTTGCC
TCACAGGAGTTAGCTGAGAAGGCGCTAGGGAAGCACAAGGAGAGAATAGGGCACAGGTATATTGAGGTGTTCAAGAGCAG
TCAGGAAGAGGTTAGGTCATACTCAGATCCCCCTCTGAAGTTTATGTCCGTGCAGCGACCAGGGCCCTATGACCGCCCCG
GCACAGCCCGGAGGTATATCGGCATTGTCAAGCAAGCAGGCCTGGAGAGGATGAGGTCTGGTGCCTACAGTGCAGGCTAT
GGGGGCTATGAGGAGTACAGTGGCCTCAGTGATGGTTACGGCTTCACCACCGACCTATTTGGAAGAGACCTCAGTTATTG
TCTCTCTGGGATGTATGACCACAGGTATGGAGATGGCGAGTTTACTGTCCAGAGCACCACTGGACACTGTGTCCACATGA
GGGGGCTGCCATACAAAGCCACTGAGAACGACATTTACAACTTCTTCTCTCCACTCAACCCCGTGAGAGTCCATATTGAG
ATTGGCCCTGATGGAAGAGTGACGGGCGAAGCTGATGTTGAGTTTGCCACCCACGATGAAGCTGTGGCAGCCATGTCCAA
AGACAGGGCCAACATGCAACACAGATACATAGAACTTTTCTTGAATTCCACAACAGGGGCCAGCAATGGGGCATATAGCA
GCCAGATGATGCAAGGCATGGGGGTGTCAACCCAGTCCACATACAGTGGCCTTGAGAGCCAGTCCGTGAGTGGCTGTTAC
GGGGCTGGCTACGGTGGCCAGAACAGCATGGGTGGATATGACTAG

Alignment

ORF - retro_sscr_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL
          MLG.EGGEGFVVK.RGLPWSCS...VQ.F.SDC.I..GA.G..FIYTREGR.SGEAFVELESED.VK.AL
Retrocopy MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIRDGAAGVHFIYTREGRQSGEAFVELESEDDVKMAL

Parental  KKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGI
          KKDRE.MGHRY.EVFKS...EMDWVLKH.GPNS.DTANDGFVRLRGLPFGC.KEEIVQFFSGLEIVPNGI
Retrocopy KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADTANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGI

Parental  TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPYD
          TLPVD..G..TGEAFVQFASQE.AEKAL.KHKERIGHRYIE.FKSS..EVR...DPP.K.M..QRPGPYD
Retrocopy TLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEVRSYSDPPLKFMSVQRPGPYD

Parental  RPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGGS
          RPG..R.Y..I...AG.ERMR.GAY..GYGGY..Y.G..DGYGF..D.FGRDL.YC.SGM.DHRYGDG..
Retrocopy RPGTARRYIGIVKQAGLERMRSGAYSAGYGGYEEYSGLSDGYGFTTDLFGRDLSYCLSGMYDHRYGDGEF

Parental  TFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKAN
          T.QSTTGHCVHMRGLPY.ATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATH..AVAAMSKD.AN
Retrocopy TVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHDEAVAAMSKDRAN

Parental  MQHRYVELFLNSTAGASGGAYGSQMLGGMGLSNQSSYGGPASQQLSGGYGGGYGGQSSMSGY
          MQHRY.ELFLNST.GAS.GAY.SQM..GMG.S.QS.Y.G..SQ..SG.YG.GYGGQ.SM.GY
Retrocopy MQHRYIELFLNSTTGASNGAYSSQMMQGMGVSTQSTYSGLESQSVSGCYGAGYGGQNSMGGY

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	274.09 RPM	82.96 RPM
SRP014902_testis	241.87 RPM	424.48 RPM
SRP018288_heart	84.61 RPM	213.29 RPM
SRP018288_kidney	215.53 RPM	311.28 RPM
SRP018288_liver	178.14 RPM	241.78 RPM
SRP018288_lung	344.48 RPM	519.82 RPM
SRP018856_adipose	364.46 RPM	266.50 RPM
SRP035408_brain	76.77 RPM	260.28 RPM
SRP035408_liver	199.74 RPM	275.56 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_70 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_70 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_70 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008888	2 retrocopies	retro_amel_57, retro_amel_9,
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Cavia porcellus	ENSCPOG00000001485	5 retrocopies	retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Felis catus	ENSFCAG00000001204	2 retrocopies	retro_fcat_131, retro_fcat_27,
Homo sapiens	ENSG00000169045	2 retrocopies	retro_hsap_3322, retro_hsap_4911,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Otolemur garnettii	ENSOGAG00000012631	2 retrocopies	retro_ogar_208, retro_ogar_498,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pongo abelii	ENSPPYG00000016121	1 retrocopy	retro_pabe_110,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Rattus norvegicus	ENSRNOG00000003399	1 retrocopy	retro_rnor_340,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Sus scrofa	ENSSSCG00000014022	1 retrocopy	retro_sscr_70 ,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,