RetrogeneDB ID: retro_chof_2092

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_48481:1092..1949(+)
• 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_2092
ATGAATATGCAAAAACAGCAAAAAAACAATGCTATCAGGTCAGTGTTTTGAACTATGAAAGAAAGATGAAAAAGAGAGGT
TTGACCCTACTCATTTTCAGGACTGTCTTATTCAAGCCTTTACTGAAGCTGGTACTGCTTTGGATTAGTAGCAAAGTTTC
TTGATGCTTCTGGAGCAAAACTTGATCATCGCTGATCTGCAGAAATACTCTTTGACATTCTGGTGGCCCGTGGAATGCTG
GCCCCAGGTGGTGCACTGGCAGATGACATTGTGCATGCAGACTCTGTGTGTTTGCAGCACAAGAAGACCTAGAGATCATG
CAAGCATTTTCTCAGGTTTTTAACAAGTTAATCAGGTGCTACTAATACCTGGAGAAAGGTTTTGAAGATGAAGTTAAAAA
GCTGCTGCTGTTCTTAATTAAAGGGTTTCTCAGAGTTGGAAAGGAAAAAGCTTGCTAAGTTATCTAGTGTTCTCCTGGCT
AACGGGACACTTAATGCATCCATTCTTGATAGCCTTTATAATGAGCATTTGGTTAAAAACAGGGTTGCAACAGCTTTTAT
TGTAAAGTTCTTTAAATCATGGTTAAATGAAAAGATGCAATATCTACAGGTCTTTGGAATGTCAGCATGGATAACAGACT
GATGGAACTTTTTCCTGCAAATAAGCAAAGCATCAAACACTTCATAAAGTATTTTACTGAGCTTGGCTTGAACAGAGCTT
TCAGAATATGTTTGGAATCAGCAAACCATAGGAGCTCATAAAGAGCTCCAGAAAAAGTTCAAGAACAGATGTCCCGTGGT
GATCCATTTAAGGATATCATTTCATATGTCAGGGAGGAGATGAAAAGAAACAACATC

Alignment

ORF - retro_chof_2092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.58 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MNNQKQQKPT-LSGQRFKTRKRDEKERFDPTQFQDCIIQGLTETGTDLE-AVAKFLDASGAKLDYRRYAE
          MN.QKQQK...LSGQ.F...K.DEKERFDPT.FQDC.IQ..TE.GT.L...VAKFLDASGAKLD.R..AE
Retrocopy MNMQKQQKNN>LSGQCFEL*KKDEKERFDPTHFQDCLIQAFTEAGTALD<LVAKFLDASGAKLDHR*SAE

Parental  TLFDILVAGGMLAPGGTLADDMMRTD-VCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKK-LL
          .LFDILVA.GMLAPGG.LADD....D..CVFAAQEDLE.MQAF.QVFNKLIR.Y.YLEKGFEDEVKK.LL
Retrocopy ILFDILVARGMLAPGGALADDIVHAD<LCVFAAQEDLEIMQAFSQVFNKLIRCY*YLEKGFEDEVKKLLL

Parental  LF-LKGFSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINE-KDINAVAA
          ...LKGFSE.ER.KLA.L..VLLANGTLNASIL.SLYNE.LVK..V..AF.VK.FKSW.NE.KD..A...
Retrocopy FL>LKGFSELERKKLAKLSSVLLANGTLNASILDSLYNEHLVKNRVATAFIVKFFKSWLNE<KD--AIST

Parental  SLRKVSMDNRLMELFPANKQSVEHFTKYFTEAGLK-ELSEYVRNQQTIGARKELQK-ELQEQMSRGDPFK
          .L..VSMDNRLMELFPANKQS..HF.KYFTE.GL..ELSEYV.NQQTIGA.KELQK...QEQMSRGDPFK
Retrocopy GLWNVSMDNRLMELFPANKQSIKHFIKYFTELGLN>ELSEYVWNQQTIGAHKELQK<KVQEQMSRGDPFK

Parental  DIILYVKEEMKKNNI
          DII.YV.EEMK.NNI
Retrocopy DIISYVREEMKRNNI

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_2092 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,