RetrogeneDB ID: retro_chof_2309

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_65040:6606..7214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM1
• Ensembl ID: ENSCHOG00000012788
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_chof_2309
GAGGGTGATGTGGCAGCCCTCAATCGCTGCGTACAGCTCGTTGAGGAAGAGTCGGACAGGCCCCAAGAGCACCTGGCCAC
AGCCCTGCAGAAGCTGGAGGGGTCCGAAAAGGCTGCCGATGAGAGCAAGTGGGGAATGAAGGTGACAGAGAACCAGGCCA
CGGAGGGCGAGAAGATGGAGATCCAGGAGCTGCAGCTCAAATGGGCCAAACACATCGCCGAGGAAGCCGACCTCAAATAC
AAGGAGGTAGCCTGGAAGTTGGTCATTCTGGAGGGTGAGCTGCAGAGAGCCGAGGAGCGGGCGGAAGTGTCTGAACTAAA
ATGCGGTGACCTGGTGGAGGAGCAGCTCAAGACCGTCACCAACGACCTCAAGTCACTAGAAGCTGCCTTGAAGAAGTATT
CTGAAAAGGAGGGTAAATATGAAGAAGAGCTCAAACTTCTGTCTGACAAGCGGAAAGAGGCTGAGACCCACGCCGAATTC
ACAAAGACAACAGTTGTAAAACTGGAAAAGACGATCGACAACCTGGAAGAAAAACGTGCCCAGGCCAAAGAAGATTAAGT
GGGCTTACGTCAGACACTGGTCAGACGCTAAATGAACTTAACTCTTTA

Alignment

ORF - retro_chof_2309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.8 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEA
          E.DVA.LNR..QLVEEE.DR.QE.LATALQKLE..EKAADES..GMKV.E..A...E.KMEIQE.QLK.A
Retrocopy EGDVAALNRCVQLVEEESDRPQEHLATALQKLEGSEKAADESKWGMKVTENQATEGE-KMEIQELQLKWA

Parental  KHIAEDADRKYEEVARKLII-ESDLERAEERAELSEGKCAEL-EEELKTVTNNLKSLEAQAEKYSQKEDK
          KHIAE.AD.KY.EVA.KL.I.E..L.RAEERAE.SE.KC..L.EE.LKTVTN.LKSLEA...KYS.KE.K
Retrocopy KHIAEEADLKYKEVAWKLVILEGELQRAEERAEVSELKCGDLVEEQLKTVTNDLKSLEAALKKYSEKEGK

Parental  YEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEEKVAHAKEENLSMHQML-DQTLLELNNM
          YEEE.K.LSDK.KEAET.AEF....V.KLEK.ID.LEEK.A.AKE......Q.L..QTL.ELN..
Retrocopy YEEELKLLSDKRKEAETHAEFTKTTVVKLEKTIDNLEEKRAQAKED*VGLRQTL<GQTLNELNSL

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_2309 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309 , retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,