RetrogeneDB ID: retro_dord_44

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1222:38164..38679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000000671
• Aliases: None
• Description: None

Sequence

>retro_dord_44
GTAGGCATAGCTGCTAAATTCATCACCCAGGTATCCCCAGGGGAGTGTAATGAAGTATTCAATGATGTTTGACTCCTACT
TAAAAATGAGAATCTCCTCAGGGAAGGGGCAGCACATGCATTTGCCCAGTATAACTTGGATCAATTCACACCTGTGAAGA
TAGAAGGATACAAAGATCAGGTCCTAATAACAGAGCACGATGACCTAGCTAATAGCAGATTTTTAGATCCAAGGAACAAA
ATTTCCTTTAAGTTTGATCACTTACCGAAAGAGCAAGTGACCCCCAGCCACAGGAAGTAGATGGAGGTTTGAAGTCTTGG
AGAGAATCCTGTGACAGTGCTTTAAGAGCCTACATGAAACATCATTATTCCAACAGCTTCTTTACTGTTTATGCTAAAAC
TATAGATAAGCAACAGACTATAATTGTGTGTATTGAAAGCCACCAGTTTCAGCCTAAAAACTTGTGGAATAGTTGTTGGA
GATCAGAGTGGAAGTTCACAGTCACACCACCTACA

Alignment

ORF - retro_dord_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.55 %
• Parental protein coverage: 63.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLG
          V.IAAKFIT...PGE.NEVFNDV.LLL.N.NLLREGAAHAFAQYN.DQFTPVKIEGY.DQVLITEH.DL.
Retrocopy VGIAAKFITQVSPGECNEVFNDV*LLLKNENLLREGAAHAFAQYNLDQFTPVKIEGYKDQVLITEHDDLA

Parental  NSRFLDPRNKISFKFDHLRKE-ASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTVYAKTIDGQQ
          NSRFLDPRNKISFKFDHL.KE.ASDPQP.EVDGGLKSWRESCDSALRAY.K.HYSN.F.TVYAKTID.QQ
Retrocopy NSRFLDPRNKISFKFDHLPKE<ASDPQPQEVDGGLKSWRESCDSALRAYMKHHYSNSFFTVYAKTIDKQQ

Parental  TIIACIESHQFQPKNFWNGRWRSEWKFTITPPT
          TII.CIESHQFQPKN.WN..WRSEWKFT.TPPT
Retrocopy TIIVCIESHQFQPKNLWNSCWRSEWKFTVTPPT

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_44 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 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44 ,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,