RetrogeneDB ID: retro_cfam_230

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:3670454..3671699(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007044
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSCAFG00000000336
• Aliases: HNRNPH1, HNRPH1
• Description: heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]

Sequence

>retro_cfam_230
ATGATGCTGGGCCCCGAGGGAGGTGAAGGCTTTGTGGTCAAGCTCCGTGGCCTGCCCTGGTCCTGCTCTGTTGAGGATGT
GCAGAATTTCCTTTCTGACTGCACAATTCATGATGGGGCTGCAGGCGTTCATTTCATCTACACTAGAGAAGGCAGGCAGA
GTGGTGAGGCTTTTGTTGAACTTGAATCAGAAGATGATGTAAAAATGGCCCTTAAAAAAGACAGGGAAAGCATGGGACAC
CGGTACATTGAGGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGTGGTCCAAACAGTGCCGACAC
CGCCAATGATGGCTTCGTGCGGCTTCGAGGACTCCCATTTGGATGCACCAAGGAAGAAATCGTTCAGTTCTTCTCAGGGT
TGGAAATTGTGCCAAACGGGATCACACTGCCTGTGGACCCCGAGGGCAAGATTACAGGGGAAGCCTTTGTGCAGTTTGCC
TCCCAGGAGTTAGCTGAGAAGGCCCTCGGGAAGCACAAGGAGAGAATAGGGCACAGATATATTGAAGTGTTTAAGAGCAG
TCAGGAAGAAGTTAGGTCATACTCAGATCCTCCTCTGAAGTTCATGTCTGTACAGCGGCCGGGGCCCTATGACCGCCCTG
GCACAGCCAGGAGGTATATTGGCATTGTCAAGCAAGCAGGCCTGGAGAGGATGAGGTCTGGTGCTTATAGTGCAGGCTAT
GGGGGCTATGAGGAGTACAGTGGCCTCAGCGATGGCTACGGCTTCACCACTGATCTGTTCGGGAGAGACCTCAGCTACTG
TCTCTCGGGCATGTATGACCACAGATATGGAGATGGCGAGTTCACCGTCCAGAGCACCACTGGACACTGTGTCCACATGA
GAGGGCTGCCGTACAAAGCTACCGAGAACGACATTTACAACTTCTTCTCTCCACTCAACCCTGTGAGAGTCCATATTGAG
ATTGGCCCTGATGGAAGAGTGACGGGTGAAGCTGATGTTGAGTTTGCCACTCACGAAGAAGCTGTGGCAGCTATGTCCAA
AGACCGGGCCAACATGCAACACAGATACATAGAACTTTTCCTGAATTCCACAACTGGGGCCAGCAATGGGGCATATAGCA
GCCAGATGATGCAAGGCATGGGAGTGTCAGCCCAGTCGACTTACAGTGGCCTCGAGAGCCAGTCTGTGAGTGGCTGTTAC
GGGGCTGGCTATGGAGGCCAGAACAGCATGGGTGGATATGACTAG

Alignment

ORF - retro_cfam_230 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.06 %
• Parental protein coverage: 93.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
          MMLG.EGGEGFVVK.RGLPWSCS...VQ.F.SDC.I..GA.G..FIYTREGR.SGEAFVELESED.VK.A
Retrocopy MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELESEDDVKMA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          LKKDRE.MGHRY.EVFKS...EMDWVLKH.GPNS.DTANDGFVRLRGLPFGC.KEEIVQFFSGLEIVPNG
Retrocopy LKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADTANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNG

Parental  ITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
          ITLPVD..G..TGEAFVQFASQE.AEKAL.KHKERIGHRYIE.FKSS..EVR...DPP.K.M..QRPGPY
Retrocopy ITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEVRSYSDPPLKFMSVQRPGPY

Parental  DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
          DRPG..R.Y..I...AG.ERMR.GAY..GYGGY..Y.G..DGYGF..D.FGRDL.YC.SGM.DHRYGDG.
Retrocopy DRPGTARRYIGIVKQAGLERMRSGAYSAGYGGYEEYSGLSDGYGFTTDLFGRDLSYCLSGMYDHRYGDGE

Parental  STFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
          .T.QSTTGHCVHMRGLPY.ATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHE.AVAAMSKD.A
Retrocopy FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRA

Parental  NMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYANQSS--YG-GPASQQLSGGY
          NMQHRY.ELFLNST.GAS.GAY..........S......G......S..YG.G...Q...GGY
Retrocopy NMQHRYIELFLNSTTGASNGAYSSQMMQGMGVSAQSTYSGLESQSVSGCYGAGYGGQNSMGGY

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
SRP012049_cerebellum	93.99 RPM	330.78 RPM
SRP017611_brain	42.24 RPM	127.90 RPM
SRP017611_kidney	213.04 RPM	135.71 RPM
SRP017611_liver	92.67 RPM	131.61 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_230 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM537878	3670502	3671011	99.9	508	1	507

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_230 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Canis familiaris	ENSCAFG00000000336	2 retrocopies	retro_cfam_200, retro_cfam_230 ,
Canis familiaris	ENSCAFG00000009305	1 retrocopy	retro_cfam_1096,
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,
Dipodomys ordii	ENSDORG00000005453	1 retrocopy	retro_dord_3,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Gorilla gorilla	ENSGGOG00000025844	2 retrocopies	retro_ggor_1299, retro_ggor_177,
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,
Mustela putorius furo	ENSMPUG00000000693	1 retrocopy	retro_mputfur_156,
Mus musculus	ENSMUSG00000007850	1 retrocopy	retro_mmus_142,
Nomascus leucogenys	ENSNLEG00000026658	3 retrocopies	retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,