RetrogeneDB ID: retro_chof_1018

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_1844:6410..7152(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSCHOG00000004622
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_chof_1018
ATGAAGCTGAACATCTCCTTCCCAGCCACTGGCTGCCAGAAGCTCATTGAAGCAGACGATGAACGCAAACTTTGTACATT
TTATGAGAAGTGTATGGCCACAGAAGTTGCTGCTGATGCCCTCGGTGAAGAGTGGAAGGGTTATGTTGTCCAAGTCAGTG
GTGGAAATGACAAACAAGGTTTCCCCATGAAATAGTATCTTGACCCATGGCTGTGTCTACCTCTTACAGAGAAAGGGGCA
TTCCTGTTATAGACCAAGGAGAACTGGAGAAAGAAAGTGCAGATGTGCTCGGGGTTGCATTGTGGATGCCAATCTGAGTG
TTCTCAACCTGGTTATTGTAAAAAAAGGAGAGAAGGATATTCCTGGACTGACTGATACTACTGTGCCTTGTTGTCTGGGG
CCCAGAAGAGCTAGCAGAATCCGCAAACTTTTCAGTCTCTCTAAAGAAGATGATGTCCGCCAGTATGTTATGAGAAAGCC
CCTGAACAAAGAAAGTAAGAAACCCAGGACCAAAGCACCCAAGATTCAGCGTCTTGTTACTCCATGCGTTCTGCAGCATA
GTCGGAGTATTGCATTGAAGAAACAGCATACTAAGAAAAACAAGGAAGAGGTTGCAGAATATGCTAAACTTTTGGCCAAG
AGAATGAAGGAGGCCAAAGAAAAACGCCAGGAACAGATTGCCAAGAGTTGGAAGCTGTCCTCACTGACAGCTTCTACCTC
TAAGTCTGAGTCCAGTCAAAAA

Alignment

ORF - retro_chof_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG-FPMK-QGVL
          MKLNISFPATGCQKLIE.DDERKL.TFYEK.MATEVAADALGEEWKGYVV..SGGNDKQG.FP......L
Retrocopy MKLNISFPATGCQKLIEADDERKLCTFYEKCMATEVAADALGEEWKGYVVQVSGGNDKQG<FPHE<NSIL

Parental  THGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRA
          THG.V.LL..KGHSCYRPRRTGERK....RGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVP..LGP.RA
Retrocopy THGCVYLLQRKGHSCYRPRRTGERKCRCARGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPCCLGPRRA

Parental  SR-RKL--LSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAE
          SR.RKL..LSKEDDVRQYV.RKPLNKE.KKPRTKAPKIQRLVTP.VLQH..R.IALKKQ.TKKNKEE.AE
Retrocopy SRIRKLFSLSKEDDVRQYVMRKPLNKESKKPRTKAPKIQRLVTPCVLQHS-RSIALKKQHTKKNKEEVAE

Parental  YAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK
          YAKLLAKRMKEAKEKRQEQIAK...LSSL.ASTSKSESSQK
Retrocopy YAKLLAKRMKEAKEKRQEQIAKSWKLSSLTASTSKSESSQK

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1018 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,