RetrogeneDB ID: retro_dord_745

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_72511:1870..2403(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps4x
• Ensembl ID: ENSDORG00000008571
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:MGI Symbol;Acc:MGI:98158]

Sequence

>retro_dord_745
ATGGCTGGTGGTCCCAAGAAGCACCTGAAGTGGGTAGCCACTCCCAAGCATTGAATGTTGGATAAACTGACCGATGTGTT
TGCTCCCTGTCCATCTACCGGTCCCCACAAGCTGAGAGAATGTCTGCTTCTCATCAGTTTCCTCAGGAACAGGCTTAAGT
ATGCCTTGACAGGAGATGAAGTGAAGAAAATCTGCATGCAGCAGCGTTTCATTAAGATTGACTGCAAAGTCAGACCTGGT
ACCACCTACCCTGCTAGTTTTACAGATGGCTTCAGCATCGATAAGACTGGGGAGAATTTCCACCTGATCTATGACACCCA
GGGTCGCTTTGCTGTTCACTGCATAACACCAGAGGAGGCCAAGTACAAGTTGTGCAAAGTGAGAAAAATCTTTGTGGGCA
CAAAAGGAATCCCTCATCTAGTAACTCATGATGCTAACCATTCACTACCCAGATCCCCTCTTCAAGGTCAATGGACACAA
TTCAAATTGATTTGGAGACCGGCAAGATAACAGATTTCATCAAATTTGACACC

Alignment

ORF - retro_dord_745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 67.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQ-RF
          MA.GPKKHLK.VA.PKH.MLDKLT.VFAP.PSTGPHKLRECL.LI.FLRNRLKYALTGDEVKKICMQ.RF
Retrocopy MAGGPKKHLKWVATPKH*MLDKLTDVFAPCPSTGPHKLRECLLLISFLRNRLKYALTGDEVKKICMQQRF

Parental  IKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
          IKID.KVR...TYPA.F.D..SIDKTGENF.LIYDT.GRFAVH.ITPEEAKYKLCKVRKIFVGTKGIPHL
Retrocopy IKIDCKVRPGTTYPASFTDGFSIDKTGENFHLIYDTQGRFAVHCITPEEAKYKLCKVRKIFVGTKGIPHL

Parental  VTHDARTIRYPDPL-IKVNDTIQIDLETGKITDFIKFDT
          VTHDA.......PL.....DTIQIDLETGKITDFIKFDT
Retrocopy VTHDANHSLPRSPL<SRSMDTIQIDLETGKITDFIKFDT

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_745 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 16 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Dipodomys ordii	ENSDORG00000008571	4 retrocopies	retro_dord_289, retro_dord_650, retro_dord_68, retro_dord_745 ,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Myotis lucifugus	ENSMLUG00000011685	5 retrocopies	retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Tarsius syrichta	ENSTSYG00000003137	16 retrocopies	retro_tsyr_1159, retro_tsyr_1167, retro_tsyr_118, retro_tsyr_1302, retro_tsyr_1333, retro_tsyr_1774, retro_tsyr_1792, retro_tsyr_1931, retro_tsyr_1936, retro_tsyr_2116, retro_tsyr_409, retro_tsyr_440, retro_tsyr_522, retro_tsyr_529, retro_tsyr_750, retro_tsyr_917,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,