RetrogeneDB ID: retro_chof_602

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_125747:3459..4097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSCHOG00000012658
• Aliases: None
• Description: transcriptional adaptor 1 [Source:HGNC Symbol;Acc:30631]

Sequence

>retro_chof_602
TACTGAGCTAACCTAAAGTTGTAGTTTAAGCAGAAGATCAGCAAAGAAGAGTTTGACCTTGAAACTCATAGACTTACCAC
ACTGGATAATGTCCATTTCCACAATGATTTCCTCCTGGCTATTCGCACATGTTGTCAGATCTTGGTTTCAACACTAGAGG
GTGCTGGATCTTTACCCTGGACAGGAGATTCTGCAGCCAAAACTGGGAAACCCAAGGGAAAGAGAAAGTTTTCTTCAGTT
CATCAGAAATTTGATCATAGATTTCAGCCTCAAAATCCCCTCTCAGGAGCCCAGCAGTTTGTGGCAAAGGATCCTCAAGT
TGATGATGACTTGAAACTTTGTTCCCATACAATGGTGCTTCCCACTCATGTCAGCTTTGAGGGAGAATGATAGTGGCTGC
TTATGAGCACGGGCTGGACAATGTCACCAAGGAGGCTCTCTCAGCTGTTGTCCACACAGTAGAGGATTACGTTAAAGATA
TTCTGACATCGGTTGTGCCAAGAAGGAAAGTTTATCAATTATGAGATGGTTGTTTTAAATATGCTTTTAGTAGTAATGTG
ATCCCTCAGCCATATCTGAATAGTGTAGTATTACAACAATTTAATAGAAAGCCCTCCAGCCTTTTCAGCTCCCTCTGC

Alignment

ORF - retro_chof_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.88 %
• Parental protein coverage: 70.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YWVNLKLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTRCQILVTP--GAGSLPWTGGSAAKPGK
          Y..NLKL.FKQKISKEEFDLE.HRL.T.DNVH.HNDFLLAI.T.CQILV....GAGSLPWTG.SAAK.GK
Retrocopy Y*ANLKL*FKQKISKEEFDLETHRLTTLDNVHFHNDFLLAIRTCCQILVSTLEGAGSLPWTGDSAAKTGK

Parental  PKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKLCSHTMMLPTR-GQLEGRMIVTAYEHGL
          PKGK.K.SSV.QKFDHRFQPQNPLSGAQQFVAKDPQ.DDDLKLCSHTM.LPT...QL.GRMIV.AYEHGL
Retrocopy PKGKRKFSSVHQKFDHRFQPQNPLSGAQQFVAKDPQVDDDLKLCSHTMVLPTH<CQL*GRMIVAAYEHGL

Parental  DNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAFGNNVTPQPYLKNSVVAYNSLIESPPA
          DNVT.EA.SAVV..VE...KDILTSVV.RRK.Y.L.DG.FKYAF..NV.PQPYL.NSVV...........
Retrocopy DNVTKEALSAVVHTVEDYVKDILTSVVPRRKVYQL*DGCFKYAFSSNVIPQPYL-NSVVLQQFNRKPSSL

Parental  FSAPC
          FS..C
Retrocopy FSSLC

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_602 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602 ,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,