RetrogeneDB ID: retro_chof_2431

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_74560:3271..4595(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD7
• Ensembl ID: ENSCHOG00000009355
• Aliases: None
• Description: bromodomain containing 7 [Source:HGNC Symbol;Acc:14310]

Sequence

>retro_chof_2431
CAGAAAGTGGAAAAAGAGAAAGGAGAGAAACAGTTTCCAGGGTAAGATAAGGGGAGTACGCATAGAAGAGTAAAGGAGGA
TAAAAAGAAGGGAGATCAAGACCGCATGAAGAATGATACAGAAAAAGACCTCCAGTATCAGGCCCTGGTAAAATTAGACC
TGCATCCTGAGAAGCCCCTCAAAAACTCTTTGGCAAGCAAGAAGTAGAGCAGACACCCATTCAAGAAGCTTTGAATCAAC
TGATGAAACAATTGCAAAATGACCCAAGTGCTTTCTTTTCATTTCCTGTGACTGATTTTATTGTTCCCAGCTACTCCATG
ATCATTAAACACCCAATGGATTTTAGAACCATGAAAGAAAAGATCAAGAACAGTAACTATCAGTCCATAGAAGAATTAAA
GATAACTTCAAATTAATGTGTGCTAATTCCATGATTTACAGCAAACCAGAGACAATTTATTATAAAGCTGCAAAGAAGCT
ATTGTACGTGGGAATGAAAATTCTTAGCCAGGAAAGAATTCAGAGCCTGAAAAAGAGCATAGACTTCATGACAGACTTGC
AAAAAAACTCAAAAACAGAAAGATAGAGCAGACACATTGCAGAATGGGGAGGAGAGTGGCTGCTGGCCCAGAGAGAGGGA
AGACTCTAGTGATATGGAAGCCCAAGTATTCAGAAACCCCAATAAGGAAAACAAAAAGACATGCTTGAATATTAATTTAA
AAGCAGTAATTTAGACAGAGAGCAGGATCAGATTGACTGTATTGTTAAAGAGCCTAGAGGAACTAGAGGAAAGCTAACCA
GGCAGTTGGTTAACAGTCACTGTGAATTTGAAAGAAGAAAACCAGATGGGACAACAACATTGGGACTTCTCCATTCTGTG
GATCCATTGTCGGGGAACAAGGCTACTGCCATGTAAGACTGGAGATGACAACTGGAAGACTTCAGTTTGGAGTGAATACT
TGCAGAGGTTCAAAGGAGATAAAAGAAACCAAGTAACTCCAGTGTTATTATGCTTGAGTTACAGACCCTACAGTTCTTGT
GAACCACATTGTGACTCCACATTTGCAAATATCAGCAAGGATGATTCTGATTTAATCTTTTGGCCTACGAGGAAGATTCT
CATCTTCCAAGCAGTTTCAGTACCCATAAGTTTTGGGCCACTTGCCAAGATTGTCCATATGTTATGGCAGACAGGTTGCT
GGGTAGTTTAACAAAAGGAGGGCATTCTAGAACCCTACAAGAGTTGGAAATGACATCACATGAGGACAAAGGCAAGACTG
CGCCACTTGACGCACTAGAGGACACGGAGGATTTTGTTTCTCTC

Alignment

ORF - retro_chof_2431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.81 %
• Parental protein coverage: 69.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KRKKRKKGEKQVPGEEKGRKRRRVKEDKKKRDRDRMEDDGEKDLQCQT-PRLDLPPEKPLTSSLA-KQKV
          ......KGEKQ.PG..KG...RRVKEDKKK.D.DRM..D.EKDLQ.Q....LDL.PEKPL..SLA.KQ.V
Retrocopy QKVEKEKGEKQFPG*DKGSTHRRVKEDKKKGDQDRMKNDTEKDLQYQALVKLDLHPEKPLKNSLA<KQEV

Parental  EQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIRNNDYQSIEELK-DNF
          EQTP.QEALNQLM.QLQ..DPSAFFSFPVTDFI.P.YSMIIKHPMDF.TMKEKI.N..YQSIEELK.DNF
Retrocopy EQTPIQEALNQLMKQLQN-DPSAFFSFPVTDFIVPSYSMIIKHPMDFRTMKEKIKNSNYQSIEELK<DNF

Parental  KLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADLQK-TRKQKDRADTSQSGEDS
          KLMC.N.MIY.KPETIYYKAAKKLL..GMKILSQERIQSLK.SIDFM.DLQK.T.KQKDRADT.Q.GE.S
Retrocopy KLMCANSMIYSKPETIYYKAAKKLLYVGMKILSQERIQSLKKSIDFMTDLQK>TQKQKDRADTLQNGEES

Parental  SCWPREREDSGDVEAQAFKSPNKENKK-RDKDMLEDKLKNSNLEREQEQIDRIVKE---SGGKLTRRLIN
          .CWPREREDS.D.EAQ.F..P...NK....KDMLE...K.SNL.REQ.QID.IVKE.....GKLTR.L.N
Retrocopy GCWPREREDSSDMEAQVFRNP---NKE<KQKDMLEY*FKSSNLDREQDQIDCIVKEPRGTRGKLTRQLVN

Parental  SQCEFERRKPDGTTTLGLLLPMDP-IVGDPGYCPVRLGMTTGRLQSGVNT-LQGFKEDKRNKVTPVLY-L
          S.CEFERRKPDGTTTLGLL...DP.IVG..GYC.VRL.MTTGRLQ.GVNT.LQ.FK.DKRN.VTPVL..L
Retrocopy SHCEFERRKPDGTTTLGLLHSVDP<IVGEQGYCHVRLEMTTGRLQFGVNT<LQRFKGDKRNQVTPVLLCL

Parental  NYGPYSSYAPHYDSTFANISKDDSDLIY-SAYGEDTELASDFSIHEFLATCQDYPYVMADSLLDVLTKGG
          .Y.PYSS..PH.DSTFANISKDDSDLI...AY.ED..L.S.FS.H.F.ATCQD.PYVMAD.LL..LTKGG
Retrocopy SYRPYSSCEPHCDSTFANISKDDSDLIF<LAYEEDSHLPSSFSTHKFWATCQDCPYVMADRLLGSLTKGG

Parental  HSRTLQELEMSSPEDEGQTGTLDTAKDMEQVTEI
          HSRTLQELEM.S.ED.G.T..LD...D.E.....
Retrocopy HSRTLQELEMTSHEDKGKTAPLDALEDTEDFVSL

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_2431 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009355	1 retrocopy	retro_chof_2431 ,
Callithrix jacchus	ENSCJAG00000001832	1 retrocopy	retro_cjac_2372,
Homo sapiens	ENSG00000166164	2 retrocopies	retro_hsap_2723, retro_hsap_3507,
Gorilla gorilla	ENSGGOG00000014824	2 retrocopies	retro_ggor_1895, retro_ggor_2372,
Monodelphis domestica	ENSMODG00000013057	1 retrocopy	retro_mdom_152,
Otolemur garnettii	ENSOGAG00000011289	2 retrocopies	retro_ogar_326, retro_ogar_438,
Pan troglodytes	ENSPTRG00000008103	3 retrocopies	retro_ptro_1840, retro_ptro_2379, retro_ptro_2384,