RetrogeneDB ID: retro_chof_458

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_11136:16831..17419(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSCHOG00000001247
• Aliases: None
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_chof_458
GGACTATCAACTGATAAAGACTCTGAAGAAAAGAAAAAAGAACCTGCCATGACATCGCAGAACAGCCCTGAAGCTTGAGA
GAAAAGTAGCTCTAGTGGCAACGTAAGCATCAGAAAGGATGAGGCAAATGCTCGAGATACTTACGTTTCATCTTTTCCTC
GGGCACCAAGCACTTCTGATTCTGTACGGTTAAAGTATAGGGAGATGCTTGCCGCAGCTCTCCGAACAGGAGATGACTAC
ATTGCTATTGGAGCTGATGAGGAAGAATTAGGATCTCAAATTGAGGAAGCTATATATCAAGATATAAGGAACACGGACAT
GAAATACAAAAATAGAGTACGAAGTAGGATATCAAATCTTAAGGATGCAAAGAATCCAAATTTAAGGAAAAATGTACTGT
GTGGGAATATTCCTCCTGACTTATTTGCTAGAATGACAGCAGAGGAAATGGCAAGTGATGAGCTCAAAGAGATGCAGAAA
AACTTGACCAAAGAAGCCATCAGAGAGCATCAAATGGCCAAAACGGGTGGAACCCAGACTGACTTGTTCACATGTGGCAA
ATGTAAAAAGAACTGTACTTATACACAG

Alignment

ORF - retro_chof_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.79 %
• Parental protein coverage: 71.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPSTDKDSEEKKKEPAMTSQNSPEAREESSSSGNVSSRKDEANARDTYVSSFPRAPSTSDSVRLKCREML
          G.STDKDSEEKKKEPAMTSQNSPEA.E.SSSSGNVS.RKDEANARDTYVSSFPRAPSTSDSVRLK.REML
Retrocopy GLSTDKDSEEKKKEPAMTSQNSPEA*EKSSSSGNVSIRKDEANARDTYVSSFPRAPSTSDSVRLKYREML

Parental  AAALRTGXXXXXXXXXXXXXXXXXXXXIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPD
          AAALRTG....................IYQ.IRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPD
Retrocopy AAALRTGDDYIAIGADEEELGSQIEEAIYQDIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPD

Parental  LFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQ
          LFARMTAEEMASDELKEM.KNLTKEAIREHQMAKTGGTQTDLFTCGKC.KKNCTYTQ
Retrocopy LFARMTAEEMASDELKEMQKNLTKEAIREHQMAKTGGTQTDLFTCGKC-KKNCTYTQ

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_458 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 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458 ,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,