RetrogeneDB ID:

retro_chof_1890

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_415754:3..559(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAZ
Ensembl ID:ENSCHOG00000002798
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]


Retrocopy-Parental alignment summary:






>retro_chof_1890
ATGGGTAAAAATGAGCTGGTGCAGAAGGCCAAACTGGCTGAACAGGCTGAGTGATATGATCACATGGCAGCCTGCATGAA
GTCTGCAACTGAGCAAGAGCTGAATTATTCAATGAGGAGAGGAATCTTCTCTTGGTTGCTTACAAAAATGTTGTAGGAGC
TCTTAGGCCATCTTGGAAGGTTGTCTAAAGTATTGAGCAAAAGATGGAAGGTAGTGAGAAAAAGCAGCAGATGGCTCAAG
AATACAGAGAGAAAATTGAGAATGAGCTAAGAAATATCTGCAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATCCCC
CATGCCTCACAAGCAGAGAGAAAAGTCTTCTATTTGAAAATGAAAGGAGACTACTATCCTTACTTGGCTGAGGTTGCTGC
TGGTGATGACAAGAAAGGGATTGTGGATCAGTCACAACAAGCATACGAAGAAGCATTTGAAATCAGAAAAAGGAAATGCA
ACCAATGCATCCTATCAGGTTGGGTCTAGCTCTTAGGTTCTATTATAAGATACTGAACTCCCCTGAGAAAGTCTGC

ORF - retro_chof_1890 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.25 %
Parental protein coverage: 82.53 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMDKNELVQKAKLAEQAERYDDMAACMKSVTEQG-AELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKT
M.KNELVQKAKLAEQAE.YD.MAACMKS.TEQ..AEL.NEERNLL.VAYKNVVGA.R.SW.VV.SIEQK.
RetrocopyMGKNELVQKAKLAEQAE*YDHMAACMKSATEQE<AELFNEERNLLLVAYKNVVGALRPSWKVV*SIEQKM
ParentalEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKX
EG.EKKQQMA.EYREKIE.ELR.ICNDVLSLLEKFLIP.ASQAE.KVFYLKMKGDYY.YLAEVAAGDDK.
RetrocopyEGSEKKQQMAQEYREKIENELRNICNDVLSLLEKFLIPHASQAERKVFYLKMKGDYYPYLAEVAAGDDKK
ParentalXIVDQSQQAYQEAFEI-SKKEMQPTHPIRLGLALNFSVFYYEILNSPEKAC
.IVDQSQQAY.EAFEI..KKEMQP.HPIRLGLAL.F...YY.ILNSPEK.C
RetrocopyGIVDQSQQAYEEAFEI<QKKEMQPMHPIRLGLALRF---YYKILNSPEKVC

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_1890 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 27 parental genes, and 124 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
retro_acar_25, retro_acar_44,
Bos taurus ENSBTAG000000002364 retrocopies
retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris ENSCAFG000000005806 retrocopies
retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
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 ENSCHOG0000000466113 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 ENSCHOG0000000578215 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 ENSCHOG000000108612 retrocopies
retro_chof_1912, retro_chof_905,
Callithrix jacchus ENSCJAG000000158445 retrocopies
retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus ENSCPOG000000202855 retrocopies
retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Ficedula albicollis ENSFALG000000058601 retrocopy
retro_falb_13,
Felis catus ENSFCAG000000320174 retrocopies
retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Gallus gallus ENSGALG000000107251 retrocopy
retro_ggal_3,
Gorilla gorilla ENSGGOG000000221339 retrocopies
retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Loxodonta africana ENSLAFG000000049442 retrocopies
retro_lafr_1089, retro_lafr_112,
Myotis lucifugus ENSMLUG000000173233 retrocopies
retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta ENSMMUG000000064897 retrocopies
retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422, retro_mmul_2503, retro_mmul_451,
Mus musculus ENSMUSG000000222853 retrocopies
retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
retro_ocun_1091, retro_ocun_248,
Pongo abelii ENSPPYG000000187917 retrocopies
retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
retro_psin_13,
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
retro_shar_126, retro_shar_409,
Sus scrofa ENSSSCG000000060622 retrocopies
retro_sscr_222, retro_sscr_35,
Ictidomys tridecemlineatus ENSSTOG000000238643 retrocopies
retro_itri_162, retro_itri_483, retro_itri_887,
Taeniopygia guttata ENSTGUG000000120781 retrocopy
retro_tgut_4,
Tursiops truncatus ENSTTRG000000159064 retrocopies
retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos ENSVPAG000000058651 retrocopy
retro_vpac_350,


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