RetrogeneDB ID: retro_dord_3

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_8503:36033..37281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000005431
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hnrnph1
• Ensembl ID: ENSDORG00000005453
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H1 [Source:MGI Symbol;Acc:MGI:1891925]

Sequence

>retro_dord_3
ATGATGCTGGGCCCTGAGGGAGGTGAAGGCTTTGTGGTCAAACTCCGTGGCCTGCCCTGGTCCTGCTCAATTGATGATGT
GCAGAACTTTCTCTCTGACTGCACCATTCACGATGGGGTTGCAGGGGTCCATTTCATTTACACTAGGGAAGGCAGGCAGA
GTGGTGAGGCTTTTGTTGAACTTGAATCTGAAGATGATGTAAAATTGGCCCTGAAAAAAGACAGGGAAAGCATGGGCCAC
CGGTACATCGAGGTGTTCAAGTCTCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGCGGTCCAAACAGCGCTGACAG
CGCCAATGATGGCTTCGTGCGGCTCCGGGGCCTCCCGTTTGGATGCACAAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT
TAGAAATTGTGCCCAATGGGATCACACTGCCAGTGGACCCAGAGGGCAAGATTACAGGGGAGGCCTTTGTACAGTTTGCC
TCGCAGGAGTTAGCTGAGAAGGCCCTGGGGAAGCACAAGGAGAGAATAGGGCACAGGTATATCGAGGTGTTTAAGAGCAG
TCAGGAGGAAGTTAGGTCCTACTCAGACCCACCTCTGAAGTTCATGTCTGTGCAGCGCCCAGGGCCCTATGACCGGCCTG
GCACTGCCCGGAGGTACATTGGCATTGTGAAGCAGGCAGGCCTGGATCGGATGAGGTCCAGCGCCTACAGTGCAGGCTAT
GGGGGCTACGAGGAGTACAGCGGGCTCAGCGATGGCTATGGCTTCACCACCGACCTCTTTGGGCGAGACCTCAGCTACTG
TCTCTCGGGCATGTACGACCATAGATACGGGGATGGCGAGTTCACCGTGCAGAGCACCACTGGCCACTGTGTCCACATGA
GGGGGCTGCCCTACAAAGCCACCGAGAACGACATTTACAACTTCTTTTCTCCACTCAACCCTGTGAGAGTACACATTGAG
ATCGGGCCTGATGGAAGAGTGACCGGAGAGGCTGATGTGGAGTTTGCTACTCACGAAGAAGCAGTGGCAGCAATGTCAAA
AGACAGGGCCAACATGCAGCACAGATACATAGAACTCTTCCTGAATTCTACCACAGGGGCCAGCAATGGGGCATACAGCA
GCCAGGTGATGCAGGGCATGGGGGTGTCTGCCGCCCAGGCCACCTACAGTGGCCTGGACAGCCAGTCTGTGAGCGGTTGT
TACGGTACTGGCTACACCAGTCAGAACAGCATGGGTGGCTATGACTAG

Alignment

ORF - retro_dord_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 86.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
          MMLG.EGGEGFVVK.RGLPWSCS.D.VQ.F.SDC.I..G..G..FIYTREGR.SGEAFVELESED.VKLA
Retrocopy MMLGPEGGEGFVVKLRGLPWSCSIDDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          LKKDRE.MGHRY.EVFKS...EMDWVLKH.GPNS.D.ANDGFVRLRGLPFGC.KEEIVQFFSGLEIVPNG
Retrocopy LKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNG

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

Parental  DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
          DRPG..R.Y..I...AG..RMR..AY..GYGGY..Y.G..DGYGF..D.FGRDL.YC.SGM.DHRYGDG.
Retrocopy DRPGTARRYIGIVKQAGLDRMRSSAYSAGYGGYEEYSGLSDGYGFTTDLFGRDLSYCLSGMYDHRYGDGE

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

Parental  NMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGG---MGLSNQSSYGG
          NMQHRY.ELFLNST.GAS.GAY..........S.A.A......SQ...G....G...Q.S.GG
Retrocopy NMQHRYIELFLNSTTGASNGAYSSQVMQGMGVSAAQATYSGLDSQSVSGCYGTGYTSQNSMGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_3 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 30 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,
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,