RetrogeneDB ID: retro_dord_37

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1038:243281..243751(-)
• Located in intron of: ENSDORG00000007045

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps6
• Ensembl ID: ENSDORG00000012057
• Aliases: None
• Description: ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:98159]

Sequence

>retro_dord_37
AAGGAAAAACTTGAATCTGTTGGGGGCTGCATTGTGGATGCCAATCTGAGTGTTCTCAACTTGGTTATTGTAAAAAAAAA
AGGAGAAAAATATATTCCTGGACTGACAGATAACACTGTACCCCACCATCTGGACCCAAATGGGCTAGCAGAATCTGTAA
GCTCTCTAAAGAAGATGATGTCTGCCAATATGTTGTGTGAAAATCCTTGAATGAAGAAGGTAAAAAACCCATGACCAACG
CACCCAAGGTTCAGCATCTTGTGATTCCATGTGTCCTGCAACACAAACCCCGCTTTATTGCTCTGAAGAAACAACGTACT
AAGAAAAACAAGGAGGAAGCTGCAGAATATGCTAAGCTTTTGGCTAAGATAATGAAGGAAGCCAAAGAAAAACGGCAGGA
ACAGATTGCCAAGAGATGAAGGCTGTCCTCTCCAAGAGCTTCTACTTCTAAGTCTGAGTCCAGTCAAAAA

Alignment

ORF - retro_dord_37 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERKRKSVRGCIVDANLSVLNLVIVKK-GEKDIPGLTDTTVPRRL-GPKRASRIRKLFNLSKEDDVRQYVV
          ..K..SV.GCIVDANLSVLNLVI....GEK.IPGLTD.TVP..L.GPK.ASRI.K...LSKEDDV.QYVV
Retrocopy KEKLESVGGCIVDANLSVLNLVIXXXXGEKYIPGLTDNTVPHHL<GPKWASRICK---LSKEDDVCQYVV

Parental  RKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQI
          .K.LN.EGKKP.T.APK.Q.LV.P.VLQHK.R.IALKKQRTKKNKEEAAEYAKLLAK.MKEAKEKRQEQI
Retrocopy *KSLNEEGKKPMTNAPKVQHLVIPCVLQHKPRFIALKKQRTKKNKEEAAEYAKLLAKIMKEAKEKRQEQI

Parental  AKRRRLSSLRASTSKSESSQK
          AKR.RLSS.RASTSKSESSQK
Retrocopy AKR*RLSSPRASTSKSESSQK

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_37 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 11 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Choloepus hoffmanni	ENSCHOG00000004622	15 retrocopies	retro_chof_1018, retro_chof_1101, retro_chof_1107, retro_chof_1590, retro_chof_193, retro_chof_2036, retro_chof_2037, retro_chof_2051, retro_chof_2188, retro_chof_2363, retro_chof_2455, retro_chof_2486, retro_chof_2608, retro_chof_849, retro_chof_941,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dipodomys ordii	ENSDORG00000012057	2 retrocopies	retro_dord_37 , retro_dord_452,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus	ENSMLUG00000007588	27 retrocopies	retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Nomascus leucogenys	ENSNLEG00000017532	14 retrocopies	retro_nleu_1033, retro_nleu_1333, retro_nleu_1613, retro_nleu_226, retro_nleu_2471, retro_nleu_252, retro_nleu_2536, retro_nleu_2611, retro_nleu_2652, retro_nleu_2655, retro_nleu_2860, retro_nleu_313, retro_nleu_476, retro_nleu_546,
Otolemur garnettii	ENSOGAG00000016254	21 retrocopies	retro_ogar_1208, retro_ogar_1222, retro_ogar_1335, retro_ogar_1356, retro_ogar_1359, retro_ogar_1439, retro_ogar_1526, retro_ogar_1531, retro_ogar_1612, retro_ogar_1979, retro_ogar_2174, retro_ogar_2195, retro_ogar_2248, retro_ogar_2264, retro_ogar_2514, retro_ogar_2707, retro_ogar_2853, retro_ogar_3329, retro_ogar_462, retro_ogar_575, retro_ogar_782,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Tursiops truncatus	ENSTTRG00000001787	11 retrocopies	retro_ttru_1024, retro_ttru_107, retro_ttru_1275, retro_ttru_370, retro_ttru_468, retro_ttru_587, retro_ttru_748, retro_ttru_786, retro_ttru_878, retro_ttru_905, retro_ttru_934,