RetrogeneDB ID: retro_dord_433

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_183663:276..633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ssu72
• Ensembl ID: ENSDORG00000011714
• Aliases: None
• Description: Ssu72 RNA polymerase II CTD phosphatase homolog (yeast) [Source:MGI Symbol;Acc:MGI:1916241]

Sequence

>retro_dord_433
TATACCCATAATGGCATTTTGCATATGCTAAATCGAAATAAAAGAATCAAACCGGGCCCTGAAAGGTTTCAGAACTGTAA
AGATAGATTTGACCTGATACTTACATGCGAAGAGCGAGTCTATGACCTGGTGGTGGAAGACCTGAATTCCAGAGAGCAGG
AGACCTGCCAACTTGTCCATGTGGTCAACGTAGATATCCAGGACAACTATGAAGATGCCACCATTGGGTCGTTCCTCCTC
TGTGATCTCTGCCAGTGTATGCAGGAGACGGAAGACTTGGACAATGAGATTGAGGAGCTCCTTTTGGTGTTCGAGGAAAA
GACTGGCAAAGCTTTCCTGCACACCGTCTGCTTCTAT

Alignment

ORF - retro_dord_433 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVVNVDIQDNH
          YT.NGILHML.RNKRIKP.PERFQNCKD.FDLILTCEERVYD.VVEDLNSREQETCQ.VHVVNVDIQDN.
Retrocopy YTHNGILHMLNRNKRIKPGPERFQNCKDRFDLILTCEERVYDLVVEDLNSREQETCQLVHVVNVDIQDNY

Parental  EEATLGAFLICELCQCIQHTEDMENEIDELLQEFEEKSGRAFLHTVCFY
          E.AT.G.FL.C.LCQC.Q.TED..NEI.ELL..FEEK.G.AFLHTVCFY
Retrocopy EDATIGSFLLCDLCQCMQETEDLDNEIEELLLVFEEKTGKAFLHTVCFY

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_433 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 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013736	3 retrocopies	retro_amel_1930, retro_amel_292, retro_amel_84,
Canis familiaris	ENSCAFG00000019254	2 retrocopies	retro_cfam_185, retro_cfam_42,
Callithrix jacchus	ENSCJAG00000010957	3 retrocopies	retro_cjac_1640, retro_cjac_2335, retro_cjac_37,
Cavia porcellus	ENSCPOG00000002238	2 retrocopies	retro_cpor_83, retro_cpor_909,
Dipodomys ordii	ENSDORG00000011714	1 retrocopy	retro_dord_433 ,
Felis catus	ENSFCAG00000003318	1 retrocopy	retro_fcat_54,
Gorilla gorilla	ENSGGOG00000004421	1 retrocopy	retro_ggor_206,
Loxodonta africana	ENSLAFG00000002076	4 retrocopies	retro_lafr_1153, retro_lafr_1154, retro_lafr_1155, retro_lafr_400,
Myotis lucifugus	ENSMLUG00000016517	2 retrocopies	retro_mluc_292, retro_mluc_371,
Macaca mulatta	ENSMMUG00000001551	1 retrocopy	retro_mmul_159,
Monodelphis domestica	ENSMODG00000006616	3 retrocopies	retro_mdom_16, retro_mdom_1997, retro_mdom_487,
Mustela putorius furo	ENSMPUG00000014394	2 retrocopies	retro_mputfur_108, retro_mputfur_1408,
Otolemur garnettii	ENSOGAG00000024430	2 retrocopies	retro_ogar_124, retro_ogar_13,
Pongo abelii	ENSPPYG00000002000	1 retrocopy	retro_pabe_53,
Pteropus vampyrus	ENSPVAG00000017695	4 retrocopies	retro_pvam_11, retro_pvam_1151, retro_pvam_272, retro_pvam_767,
Sarcophilus harrisii	ENSSHAG00000009747	1 retrocopy	retro_shar_32,
Sus scrofa	ENSSSCG00000003348	2 retrocopies	retro_sscr_1179, retro_sscr_38,
Ictidomys tridecemlineatus	ENSSTOG00000002960	4 retrocopies	retro_itri_1055, retro_itri_1352, retro_itri_1496, retro_itri_99,