RetrogeneDB ID: retro_chof_1519

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_314076:278..1038(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000003543
• Aliases: None
• Description: None

Sequence

>retro_chof_1519
ATGAATACTCAAAAGCAGCAAAAGCCAGTGCTATCAGGCCAGCATTTCAAAGCTACGAAAAGAGATGAAAAAGAGACGTT
TGACCCTACTCAGTTTCAGGACTGTATTACTCAAGGAATAACTGAAACTGGTATTGGTTTGGAAGCAGCAGCAAAGTTTC
CTGATGCTTCTGGAGCAAAACTTGATTATTGCCGATATGCAGAAACACTCTTTGACATTCTGGTGGCTGGTGGATGCTGG
CCCCAGGTGGTGCACTGGCAGATGACATGATGCGTACAGACGTCTGCATGTTCGCAACACAAGAAGACCTAGAGACCATG
CAAGCATTTACTCAGGTTTTTAACAAGTTAATGAGGTGCTACAAATAACTGGAGAAAGGTTTTGAAGATGAAGTTAAAAA
GCTGCTGTTGTTCTTAAAGGGTTTTTCAGAGTCAGAAAGGAACAAACTGGTGTTCTCCTGGCTAACAGGACACTTAATGC
ATTCATTCTTAATAGCCTTTATAATGAGAATTTGGTTAAAGAAGGGGTTTCAGCAGCTTTTGCTGTGAAGCTCTTTTAAT
CACAGATAAATGAAAAAGATATCAATGTGGTAGCTGCAAGTCTTCAGAAAGTCAGCATGGATAACAGACTGATGGAACTT
TTTTCTGCCAATAAGCAAAGCATCGAACACTTCACAAAGTATTTTACTGAGGCAGGCTTGAAAGAGCTTTCTGAGTATGT
TCAGAATCAGCAAACCATAGGAGCTCATAAAGAGCTACAG

Alignment

ORF - retro_chof_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 73.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNNQKQQKPTLSGQRFKTRKRDEKERFDPTQFQDCIIQGLTETGTDLEAVAKFLDASGAKLDYRRYAETL
          MN.QKQQKP.LSGQ.FK..KRDEKE.FDPTQFQDCI.QG.TETG..LEA.AKF.DASGAKLDY.RYAETL
Retrocopy MNTQKQQKPVLSGQHFKATKRDEKETFDPTQFQDCITQGITETGIGLEAAAKFPDASGAKLDYCRYAETL

Parental  FDILVAGG-MLAPGGTLADDMMRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFL
          FDILVAGG.MLAPGG.LADDMMRTDVC.FA.QEDLETMQAF.QVFNKL.R.YK.LEKGFEDEVKKLLLFL
Retrocopy FDILVAGG<MLAPGGALADDMMRTDVCMFATQEDLETMQAFTQVFNKLMRCYK*LEKGFEDEVKKLLLFL

Parental  -KGFSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRK
          .KGF...........TGVLLAN.TLNA.ILNSLYNENLVKEGVSAAFAVKLF.S.INEKDIN.VAASL.K
Retrocopy <KGFFRVRKEQ----TGVLLANRTLNAFILNSLYNENLVKEGVSAAFAVKLF*SQINEKDINVVAASLQK

Parental  VSMDNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQ
          VSMDNRLMELF.ANKQS.EHFTKYFTEAGLKELSEYV.NQQTIGA.KELQ
Retrocopy VSMDNRLMELFSANKQSIEHFTKYFTEAGLKELSEYVQNQQTIGAHKELQ

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_1519 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 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519 , retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Microcebus murinus	ENSMICG00000003355	1 retrocopy	retro_mmur_831,
Myotis lucifugus	ENSMLUG00000001653	2 retrocopies	retro_mluc_1350, retro_mluc_2561,
Monodelphis domestica	ENSMODG00000015000	1 retrocopy	retro_mdom_1747,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499, retro_mmus_751, retro_mmus_990,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949,
Pteropus vampyrus	ENSPVAG00000008111	1 retrocopy	retro_pvam_773,
Tarsius syrichta	ENSTSYG00000013638	2 retrocopies	retro_tsyr_2177, retro_tsyr_483,
Tursiops truncatus	ENSTTRG00000003639	1 retrocopy	retro_ttru_153,