RetrogeneDB ID: retro_chof_671

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_133732:13..1192(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYBL2
• Ensembl ID: ENSCHOG00000000933
• Aliases: None
• Description: v-myb avian myeloblastosis viral oncogene homolog-like 2 [Source:HGNC Symbol;Acc:7548]

Sequence

>retro_chof_671
AGGCTAGGGAAGCAGTGCCGTGATCACCGGCACCACCGCTTCAACACTGAGGTGAAGCAGTCCTGCTGGACTCAGGAGGA
GGACCACACCATCAATGAGGCCCTCAGGGTGCTGGGCAACTGCTGGGCTCAGAGTGCCAAGATGCTGCCAGGGAAGAAGA
CAATGCCATGAGGAATCCATGGAGCTCCACCATCAAAAAGAAGGTGGGCATGGGAGGTCTCCTGAGAGAGTCCAGAGACT
GCAAGCCGCCCACCGTGTACTTGCTGCTGGAGATCAAAGACAAGGATGGCTGCCAGAGGGGCCACTCGGTGGAAGGCCAG
GGAAGTCTTGTGGCCACCCAGCCCCCAGCACCCCTGACCATGAAGGAAGAAGACAGCAGCGAGGAGGAGGCCACAGCAAC
CATCGTGTCTAACGAGCAGGGGCCTAGCCCTGCAGAGCCGGATAGAGTGCAGACGCCAGAGCCCATGGAGGAGTTCCCCA
AGCGGGAAGAGCAGGAGAGCTTCCTCCAGAAATGCACCTGCCCTACAAGAGGGTAGTGGAGGCTGCCAACATCTTCAATC
CTGCTGTGTGGTCCAGCCTCACTGAAGCCCTGGACTTGGTGGAGCTGGACCCTGATGCCTGGTGTGAGCTGAGATTTGAC
CTCCCTGAGGAGCTGTCTGCAGAAGGTAGCCCAGTGCAACCACCAGCACCACATCAGCAGCAGGCACTGGCACCCTGCCA
GCTTGCCGTCCTGGTACTCAGAGTGACTGAGTACCACCTGGACAGTCACACCATCTCAGGCCTGAGCCAGCACAGCCGAA
GTGAGCTGATCCCCATTTCCCTGAGCCCTGGAGTGGAGGGTTCAAGCCTTGGCACACCACTCTTGGTTCTCAAGCAGCAA
AAGAAGCATGCCACTATGCCTGCATCATGGAGAACAGCACCAGTCTGTCCTTCCTGGACCCCTGCAACAACCCCACCCCC
AAGAGCATGCCCATCAAGACCCTGCCCTTCTTGCCCTCCCAGTTTCTGAAATTCTGGAATTAACAGGACACACTGGAGCT
GCAGAGCCCCTTGCTGATGTCCACCCCAGTGTGCAGCCAGAAAATGGTGGTAACTACATCCCTGTACCGAGATAAGGTGC
CGCTGCATAAGAAACATGTCACCCCAGAGCAGATACTGCATGGGCAACACTCCCCACAT

Alignment

ORF - retro_chof_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLGKQCRERWHNHLNPEVKKSCWTEEEDRIICEAHKVLGNRWAEIAKMLPGRT-DNAVKNHWNSTIKRKV
          RLGKQCR...H...N.EVK.SCWT.EED..I.EA..VLGN.WA..AKMLPG...DNA..N.W.STIK.KV
Retrocopy RLGKQCRDHRHHRFNTEVKQSCWTQEEDHTINEALRVLGNCWAQSAKMLPGKK<DNAMRNPWSSTIKKKV

Parental  DTGGFLSESKDCKPP-VYLLLELEDKDGCQSVHPAEGQGGLVATWPLAPLAMKEEESSEEEATAATTSEE
          ..GG.L.ES.DCKPP.VYLLLE..DKDGCQ..H..EGQG.LVAT.P.APL.MKEE.SSEEEATA...S.E
Retrocopy GMGGLLRESRDCKPPTVYLLLEIKDKDGCQRGHSVEGQGSLVATQPPAPLTMKEEDSSEEEATATIVSNE

Parental  QGPIPAELDRVWTPEPMEEFPKREDQECF-PPAMSLPYKWVVEATNLLSPAVGSSFSEA-DLIESDPDAW
          QGP.PAE.DRV.TPEPMEEFPKRE.QE.F.PP.M.LPYK.VVEA.N...PAV.SS..EA.DL.E.DPDAW
Retrocopy QGPSPAEPDRVQTPEPMEEFPKREEQESF<PPEMHLPYKRVVEAANIFNPAVWSSLTEALDLVELDPDAW

Parental  CDLSKFDLPEEPSAEGSVNSSPVQPQAPRQHLALAHRQPAVLVPSVTEYRLDGHTISDLSRSSRGELIPI
          C.L..FDLPEE.SAEGS....PVQP.AP.Q..ALA..Q.AVLV..VTEY.LD.HTIS.LS..SR.ELIPI
Retrocopy CEL-RFDLPEELSAEGS----PVQPPAPHQQQALAPCQLAVLVLRVTEYHLDSHTISGLSQHSRSELIPI

Parental  SPSTEVGGSGFGTPPSVLKRQKKRRVALSPVTENSASLSFLDCNSLTPKSTP-VKTLPFSPSQFLNFWNK
          S.S..V.GS..GTP..VLK.QKK...............S........P...P..KTLPF.PSQFL.FWN.
Retrocopy SLSPGVEGSSLGTPLLVLKQQKKHATMPASWRTAPVCPSWTPATTPPPRACP<IKTLPFLPSQFLKFWN*

Parental  QDTLELESPSLTSTPVCSQKVVVTTPLHRDKTPLHQKHAAFVTPDQKYSMDNTPH
          QDTLEL.SP.L.STPVCSQK.VVTT.L.RDK.PLH.KH...VTP.Q.......PH
Retrocopy QDTLELQSPLLMSTPVCSQKMVVTTSLYRDKVPLHKKH---VTPEQILHGQHSPH

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_671 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000933	1 retrocopy	retro_chof_671 ,
Oryctolagus cuniculus	ENSOCUG00000005775	1 retrocopy	retro_ocun_1301,