RetrogeneDB ID:

retro_chof_1274

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_245220:2..1084(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCHOG00000002082
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSCHOG00000005327
Aliases:None
Description:poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]


Retrocopy-Parental alignment summary:






>retro_chof_1274
GTACGCATCATGTGGTCTCAGCATGAACCATCGCTTTGCAAAAGCGGAGTGGACAATATATTCATTAAAAATTTGGACAA
ATCTGTTGATAATAAAGCACTGTATGATACATTTTCCGCTTTTGGTAACATCCTTTCATGTAAAGTGGTTTGTGGTGAAA
ATAGTTCCAAGGACTACGGTTTTGTACATTTTGAGACACAGGAAGCAGCTGAAAGAGCTACTGAAAAATGAATGGGATGC
TTCTAAATGATCGCAAAGTATTTGTCAGGCGATTTAAGTCTCATAAAGAAGGAGAAGCCGAACTTGGAGCTAGGGCAAAA
GAGTTCACCAGTGTTTACATCAAGAATTTTGCAGAAGACATGGATGATGAGTGCCTTAAGCATCTCTTTGGCAAGTCTGG
ACCTGCTTTAAGTGTGAAAGTCATGACTGATGAAAGTGGAAAATCCAAAGGCTTTGGATTTGTGAGCTTCATAAGGCATG
AAGATGCACAGAAAGCTGTGGATGAGATGAATGGAAAGGAGCTCAATGGAAAACAAATTCACACTGGTCGAGCTCAGAAA
AAAGTGGGACAGACCGAACTTAAGCACAAATTTGAACAGATGAAGCAAGATAGGATCACTAGATACCAGGGTGTTAACCT
TTATGTGAAAACTCTTGATGATGGTATTGATGATGAACGTCTCCAGAAAGAGTTTTCTCCATTTGGTATAATCATTAGTG
CAAAGGTTATGATGGAGGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAGGAAGCTACTAAAGCA
GTTACCGAAATGAATGGTAGAATTGTGGCCACCAAGCCATTGTATGTAGCTTTAGCTCAGGGCAAAGAAGAGCGCCATGC
TCACCTCAATAACCAGTATATGCAGAGAATGGCAAGTTTAAGAGCTGTGCCCAACCCTGTAATCAATCCCTACCAGCGAG
CACCTCCTTCAGGTTACTTCATGCCAGCTATCCCACAGACTCAGAACTGTGCTGCATACTATCCTCCTAGCCAAATTGTT
CAGCTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGA

ORF - retro_chof_1274 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.35 %
Parental protein coverage: 60.77 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFETQEAA
.RIMWSQ..PSL.KSGV.N.FIKNLDKS.DNKALYDTFSAFGNILSCKVVC.EN.SK.Y.FVHFETQEAA
RetrocopyVRIMWSQHEPSLCKSGVDNIFIKNLDKSVDNKALYDTFSAFGNILSCKVVCGENSSKDYGFVHFETQEAA
ParentalDKAIEK-MIGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFIQFGKTLSV
..A.EK.M.GMLLNDRKVFV.RFKS.KE.EAELGA.AKEFT.VYIKNF.E..DDE.LK.LF...G..LSV
RetrocopyERATEK<MNGMLLNDRKVFVRRFKSHKEGEAELGARAKEFTSVYIKNFAEDMDDECLKHLFGKSGPALSV
ParentalKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQERISR
KVM.D.SGKSKGFGFVS...HEDA.KAV.EMNGKE..GK.I..GRAQKKV..Q.ELK.KFEQ.KQ.RI.R
RetrocopyKVMTDESGKSKGFGFVSFIRHEDAQKAVDEMNGKELNGKQIHTGRAQKKVG-QTELKHKFEQMKQDRITR
ParentalYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGS
YQGVNLY.K.LDD.IDDE.L.KEFSPFG.I.SAKVM.E.GRSKGFGFVCFSSPEEATKAVTEMNGRIV..
RetrocopyYQGVNLYVKTLDDGIDDERLQKEFSPFGIIISAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT
ParentalKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPA-AGGYFVPAVPQAQGSPPYYTPNQLA
KPLYVALAQ.KEER.AHL.NQYMQR.A..RA.P.N...N..Q.A...GYF.PA.PQ.Q....YY.P.Q..
RetrocopyKPLYVALAQGKEERHAHLNNQYMQRMASLRAVP-NPVINPYQRAPPSGYFMPAIPQTQNCAAYYPPSQIV
ParentalQMRPKTK-RQQGGR
Q.RP......QG.R
RetrocopyQLRPSPRWTAQGAR

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST - click to see more details

Choloepus hoffmanni was not studied using EST data.

TSS - click to see more details

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab - click to see more details

retro_chof_1274 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000024641 retrocopy
retro_chof_1943,
Choloepus hoffmanni ENSCHOG00000005327 3 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274 ,
Choloepus hoffmanni ENSCHOG000000068102 retrocopies
retro_chof_2564, retro_chof_44,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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