RetrogeneDB ID: retro_chof_136

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3064:48150..48816(-)
• Located in intron of: ENSCHOG00000013676

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSCHOG00000004661
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_chof_136
GACAATATAGCCAACTGCATGAAGGCCATGACGGAGTTGGGCACCAAGCTGTCCAACGAGGAACACAACCTGCTCTTGGT
GGCCTGCAGGAACATGGTCCAGGGCCGCAGGTCCATCTGGAGGTTTATCTTCAGCATCTAGCAGAAGACTGACTCTTCTG
GCAAGAAGTTGCAGTTGATTAGGGACTATCGGTAAAAAGTGGAGTCGGAGCTGAGATCCACCTGCACGACTGTCCTGGAA
TTGTTAGATAAGTGTTTTAATAGCCAATGCAACTAATCCAGAGAGTAAGGTCTTCTGTCTGAAAACTAGAGATTGCTTCC
TGTCCCTTGCTGAAGTGGCATGTGATGATTGAAAACAAACGATAGATAATTCCCAAGGAGTTTACCAAGAGGCGTTTGAT
GTAAGCAAGAGATGCAACCCACACACCCAGTCTGCCTGGGGCTGCCTCTTAACTTTTCTGTATTTTACTATGAGGTCCTT
AAAAACCCAGAGCTTGCTTGTACACTAGCTAAAACGGCTTTTGATGAGGCCATTGCAGAACTTGATACACTCAATGAAGA
CTCAAACAAAGACAGCACCCTCATCATGCAGTTGCTTAGAGACAACCTAACATTATGAACGTCAGATAGTACAGGAGAAG
AATGCTATGCAGCAGAAAGGGCAGAA

Alignment

ORF - retro_chof_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.48 %
• Parental protein coverage: 91.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDMATCMKPM-EQGAELFNEEHNLLSLAYNNVVRGNRSTWRVILSMEQKTNTSDKKVQLIKDYK-ENELE
          D..A.CMK.M.E.G..L.NEEHNLL..A..N.V.G.RS.WR.I.S..QKT..S.KK.QLI.DY....E.E
Retrocopy DNIANCMKAMTELGTKLSNEEHNLLLVACRNMVQGRRSIWRFIFSI*QKTDSSGKKLQLIRDYR*KVESE

Parental  LRSICTMVLELLDK-YLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKK
          LRS.CT.VLELLDK..LIANATNPESKVF.LK...D.F..LAEVAC.DD.KQTIDNSQG.YQEAFD.SK.
Retrocopy LRSTCTTVLELLDK>VLIANATNPESKVFCLKTR-DCFLSLAEVAC-DD*KQTIDNSQGVYQEAFDVSKR

Parental  EMQPTHPIRLGLALNF-SVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTL
          ...P......G..L.F.SVFYYE.L.NPELACTLAKTAFDEAIAELDTLNEDS.KDSTLIMQLLRDNLTL
Retrocopy -CNPHTQSAWGCLLTF<SVFYYEVLKNPELACTLAKTAFDEAIAELDTLNEDSNKDSTLIMQLLRDNLTL

Parental  WTSDSAGEECDAAEGAE
          .TSDS.GEEC.AAE.AE
Retrocopy *TSDSTGEECYAAERAE

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_136 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 8 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002798	9 retrocopies	retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Choloepus hoffmanni	ENSCHOG00000004661	13 retrocopies	retro_chof_136 , retro_chof_1427, retro_chof_1605, retro_chof_1835, retro_chof_2026, retro_chof_2115, retro_chof_2134, retro_chof_2233, retro_chof_429, retro_chof_481, retro_chof_489, retro_chof_527, retro_chof_863,
Choloepus hoffmanni	ENSCHOG00000005782	15 retrocopies	retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,