RetrogeneDB ID:

retro_chof_1260

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_239455:1157..2094(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MDH1
Ensembl ID:ENSCHOG00000007281
Aliases:None
Description:malate dehydrogenase 1, NAD (soluble) [Source:HGNC Symbol;Acc:6970]


Retrocopy-Parental alignment summary:






>retro_chof_1260
GAACCAGTCAGAGTCCTTGTGACTGGAGCAGCTGGCCAAATTGCATATTCACTACTGTACAGTATTGGAAATGGCTCTGT
CTTTGGTAAAGACCAGGCTTTCATTCTCGTGCTGTTGGATATCACCCCCATGATGGGGGTCCTGGAAGGGGTCCTTATGG
AACTGCAAGACTGTGCACTTCCTCTCCTAAAAGATATCATCATAACAGATAAAGAAGATGTTGCCTTCAAAGACTTGGAT
GTGGCCAGTCTTGTGGGTTCCATGCCAAGAAGGCATGGCATAGAGAGGGAAGATTTACTGAAAGCAAATGTGAAAATTTT
CAAAGTCCAAGGTGCAGCCTTGGAAAAATACGCCAAGAAGTCAGTTAAGGTTGTTGTCATAGGAAACCCAGCCAATGCTA
ACTGCCTGACAGCCTCAAAGTCAGCTCCATCCATCCCCAAGGAGAACTTCAGTTGCTTGACGCGTTTGGATCAAAACCGA
GCTAAATCTCAGATTGCTCTTAAATTTGGTGTGACTGCTGATAATGTAAAGAATGTCATCATCTGGGGAAACCATTCCTC
AACTCAGTATCCAGATGTCAACCATGCCAAGGTGAAATTGCAAGGAAAGGAAGTTGGTGTTTATGAAGCTCTGAAAGATG
ACAGCTGGCTTAACGGAGACCTCATAACGACTGTGCAGGAGCGTGGCGCTGCCATCATCAAAGGCTCGGAAACTATCCAG
CGCAATGTCCGCTGCAAAAACCATCTGTGACCACCTCAGAGATCTCTGGTTTGGAACCCAGGGGGAGTCTGTGTCCGTGG
ATGTTATGTCTGATGGCAACTCCAGTGGCATTCCTGATGATATGCTCTACTCATTCCCTGTTGTGATCAAGGATAAGACC
TGGAAGTTTGTTGCAGCTCTCCCTATTAATGATTTCTCATGTGAGAAAATGGATCTT

ORF - retro_chof_1260 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.08 %
Parental protein coverage: 93.71 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEPLRILVTGAAGQIAYSLLYSIGNGSVFGKDQPLILVLLDITPMMGVLEGVLMELQDCALPLLKDIIITD
EP.R.LVTGAAGQIAYSLLYSIGNGSVFGKDQ..ILVLLDITPMMGVLEGVLMELQDCALPLLKDIIITD
RetrocopyEPVRVLVTGAAGQIAYSLLYSIGNGSVFGKDQAFILVLLDITPMMGVLEGVLMELQDCALPLLKDIIITD
ParentalKEDVAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKVQGAALEKYAKKTVKVVVVGNPANTNCLTASK
KEDVAFKDLDVA.LVGSMPRR.G.ER.DLLKANVKIFKVQGAALEKYAKK.VKVVV.GNPAN.NCLTASK
RetrocopyKEDVAFKDLDVASLVGSMPRRHGIEREDLLKANVKIFKVQGAALEKYAKKSVKVVVIGNPANANCLTASK
ParentalSAPSIPKENFSCLTRLDQNRAKSQIALKLGVTADNVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEA
SAPSIPKENFSCLTRLDQNRAKSQIALK.GVTADNVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEA
RetrocopySAPSIPKENFSCLTRLDQNRAKSQIALKFGVTADNVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEA
ParentalLKDDSWLKGDFITTVQQRGAAVI-KARKLSSAMSAAKAICDHLRDLWFGTPEGEFVSMGVMSDGNSYGIP
LKDDSWL.GD.ITTVQ.RGAA.I.KARKLSSAMSAAK.ICDHLRDLWFGT..GE.VS..VMSDGNS.GIP
RetrocopyLKDDSWLNGDLITTVQERGAAII>KARKLSSAMSAAKTICDHLRDLWFGT-QGESVSVDVMSDGNSSGIP
ParentalDDMLYSFPVVIKNKTWKFVEGLPINDFSREKMDL
DDMLYSFPVVIK.KTWKFV..LPINDFS.EKMDL
RetrocopyDDMLYSFPVVIKDKTWKFVAALPINDFSCEKMDL

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1260 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 15 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000192951 retrocopy
Choloepus hoffmanni ENSCHOG00000007281 5 retrocopies
Callithrix jacchus ENSCJAG000000070184 retrocopies
Dasypus novemcinctus ENSDNOG000000133292 retrocopies
Homo sapiens ENSG000000146411 retrocopy
Gorilla gorilla ENSGGOG000000070851 retrocopy
Loxodonta africana ENSLAFG000000165042 retrocopies
Macaca mulatta ENSMMUG000000061632 retrocopies
Nomascus leucogenys ENSNLEG000000098231 retrocopy
Otolemur garnettii ENSOGAG000000144871 retrocopy
Pongo abelii ENSPPYG000000123731 retrocopy
Pan troglodytes ENSPTRG000000119741 retrocopy
Sorex araneus ENSSARG000000076901 retrocopy
Sus scrofa ENSSSCG000000257511 retrocopy
Tarsius syrichta ENSTSYG000000012152 retrocopies



Copyright © RetrogeneDB 2014-2017