RetrogeneDB ID: retro_chof_2239

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_60339:5612..6547(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSCHOG00000000714
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_chof_2239
GTGCCAGCACCCCCGACTCCTTCTCTACCTCCTATGGCTACCATTAACCCAGCATCTCCAGCACCAGCCTCAACAGAGCC
CCCTGCCCTGTTGCCTTCCATTGTTGTTAACTCCATTCGTTCATCCTATGTGGCAAATCAGGCATCTGCTAGGGCTGGTG
GTTGGCACAATATCAGCAAATTGATTATTGCCAAACAGATGTTACCCTCTTCTATTACCATGTCTCAAGGGGGGATGGTT
ACTGTTATCCCAGCCACAGTGTGACCTCTTGGGGGCTCCAGCTAGGCCAAACCAGTACAGCTACTATCCAACCCAGTCAA
CAAGCCCAGATAGTCACTTGGCCAGTGTTGCAGGCAGCAGCAGCAGCAGCTGCTGCTGCTTCTATGCAATTGCCTCTACC
CCGACTACAGCCGCGTCCATTACAACAGATGCCTCAGCCCCCCACTCAGCAGCAAGTGACCATACTGCAGCAGCCTCCCC
CACTCCAGGCCATGCAACAGATTCCACCTCAGAAAGTTCAAATCAATTTACACCAACAGCCACCTCCTCTGCAGATCAAA
AATATACCTCCACCCACTCTGAAAATACAGGCTAACTTAGTCCCAACAGCTGTGGAAAGCAGTCCTGAGCAGCCTATGAA
CAGCAGTCCTGAGGCCCACAGAGTGGAGACAACTACTGAGATAATCTGAGAGAAGATTACAGATATAGTTCCTGAGGTTG
AGTCTCCTCAGACAGATGTTCAGTTGGTGAGTGGCTCTCCTATGACACTCTCACCCCAGCCCTGATGAGTAAGGTCAAGT
TGTGAGAACCCTCCAGTTGTAAACAAGGACTGAGACAATGAATACTGCAGCAATGAGTGTGTGGTGAAGCACTGCAAGGA
TGTATTCCTGGCCTGGGTAGCCTTCAGAAATTGAAACACAATTGTGTTAGTGAAA

Alignment

ORF - retro_chof_2239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 50.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPAPQTPSPPPVATVNPASPAPASTEPPALSPSIVVNSTLSSYVANQASSGAGGQPNITKLIITKQMLPS
          VPAP.TPS.PP.AT.NPASPAPASTEPPAL.PSIVVNS..SSYVANQAS..AGG..NI.KLII.KQMLPS
Retrocopy VPAPPTPSLPPMATINPASPAPASTEPPALLPSIVVNSIRSSYVANQASARAGGWHNISKLIIAKQMLPS

Parental  SITMSQGGMVTVIPATV-VTSRGLQLGQTSTATIQPSQQAQIVTRSVLQAAAAAAA--SMQLPPPRLQPP
          SITMSQGGMVTVIPATV.VTS.GLQLGQTSTATIQPSQQAQIVT..VLQAAAAAAA..SMQLP.PRLQP.
Retrocopy SITMSQGGMVTVIPATV<VTSWGLQLGQTSTATIQPSQQAQIVTWPVLQAAAAAAAAASMQLPLPRLQPR

Parental  PLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQPPPLQIKNMPPPTLKMQATLVPPAVESSP
          PLQQMPQPPTQQQVTILQQPPPLQAMQQ.PPQKV.INL.QQPPPLQIKN.PPPTLK.QA.LVP.AVESSP
Retrocopy PLQQMPQPPTQQQVTILQQPPPLQAMQQIPPQKVQINLHQQPPPLQIKNIPPPTLKIQANLVPTAVESSP

Parental  ERPMNSSPETHTVETTSPEIICEMITDVVPEVESPQMDVQLVSGSPMTLSPQPRCVRSGCENPPVVSKDW
          E.PMNSSPE.H.VETT..EII.E.ITD.VPEVESPQ.DVQLVSGSPMTLSPQP..VRS.CENPPVV.KD.
Retrocopy EQPMNSSPEAHRVETTT-EII*EKITDIVPEVESPQTDVQLVSGSPMTLSPQP**VRSSCENPPVVNKD*

Parental  DNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
          DNEYCSNECVVKHC.DVFLAWVA.RN.NT.V.VK
Retrocopy DNEYCSNECVVKHCKDVFLAWVAFRN*NTIVLVK

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_2239 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239 , retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,