RetrogeneDB ID:

retro_ocun_338

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:11081886..11082458(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHA
Ensembl ID:ENSOCUG00000015939
Aliases:None
Description:lactate dehydrogenase A (LDHA), mRNA [Source:RefSeq mRNA;Acc:NM_001082277]


Retrocopy-Parental alignment summary:






>retro_ocun_338
GTTAACCTCTTTAAATTCAACATTCCTAATGTTGTCTAATACAGCTTCAGCTGCAGTTGCTTATTTCCAATTCAGTGAAT
ATCCTGACTTATGTGGCTTGGAATATAAGTGGCTTTCCCAAAACCCAGGTAATTAGAAGTGCTTGCAATCTGAAATCAGC
CTGATTCCATTGCTTAATGGGGCAAATACTGGGCGTTTACCCATTGAGCTCTCATGTGTGGATCCCCAAGAGTATGGAGA
TTCAAGTGTGCCTGTATGGAGTGGACTGAATGTTGCTGGTGTCTTGCTAAAGATTGTGCATCCAGATTAGGCACTGATGC
AGACAAAGAACAGTGGAAACAGGTTCACAAATAGGTGGTAGATAGTGCTTAGGAGGTGATCAAACTGAAAGGCTATATAT
CCTTGTCCTTTGGACCAGCTGTGGCAGATCTGACCAACATATGATGAAGAATCTCATGTGGGTGCATCCAATTTCCACCA
TAATTAAGGGTCTCTATGGAATAAAGGATGATGGCTTCCTTAGTCTTACTTCCATCTTGGGATAAAATAAAATCTCAGAT
GTTGTGAAAATG

ORF - retro_ocun_338 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.04 %
Parental protein coverage: 58.13 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVNIFKFIIPNVVKYSPHC-KLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHA
VN.FKF.IPNVV.YS..C..LL..SN.V.ILTYVAW.ISGFPK..VI.S.CNL.SA.F..LMG..LGV..
RetrocopyVNLFKFNIPNVV*YSFSC<QLLI-SNSVNILTYVAWNISGFPKTQVIRSACNLKSA*FHCLMGQILGVYP
ParentalLSCHGWI-LGEHGDSSVPVWSGMNVAGVSLKTLHPE-LGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSW
LS.H.WI...E.GDSSVPVWSG.NVAGV.LK..HP..LGTDADKEQWKQVHK.VVDSA.EVIKLKGY.S.
RetrocopyLSSHVWI<PQEYGDSSVPVWSGLNVAGVLLKIVHPD<LGTDADKEQWKQVHK*VVDSA*EVIKLKGYISL
ParentalAIGLSVADLA-ESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCVLGQNGISDVVKV
..G..VADL.....MKNL..VHPIST.IKGLYGIK.D.FLS....LG.N.ISDVVK.
RetrocopySFGPAVADLT<QHMMKNLMWVHPISTIIKGLYGIKDDGFLSLTSILG*NKISDVVKM

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 108 .17 RPM
SRP017611_kidney 0 .00 RPM 46 .12 RPM
SRP017611_liver 0 .00 RPM 113 .15 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_338 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_338 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_338 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 222 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178542 retrocopies
Bos taurus ENSBTAG000000086832 retrocopies
Choloepus hoffmanni ENSCHOG0000000997714 retrocopies
Callithrix jacchus ENSCJAG000000070941 retrocopy
Cavia porcellus ENSCPOG000000119262 retrocopies
Dasypus novemcinctus ENSDNOG0000001891511 retrocopies
Equus caballus ENSECAG000000206695 retrocopies
Echinops telfairi ENSETEG0000000750815 retrocopies
Homo sapiens ENSG000001343335 retrocopies
Gorilla gorilla ENSGGOG000000103503 retrocopies
Loxodonta africana ENSLAFG000000113071 retrocopy
Macropus eugenii ENSMEUG0000000146291 retrocopies
retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
Macaca mulatta ENSMMUG000000310242 retrocopies
Monodelphis domestica ENSMODG000000065222 retrocopies
Mus musculus ENSMUSG0000006322914 retrocopies
Nomascus leucogenys ENSNLEG000000177674 retrocopies
Oryctolagus cuniculus ENSOCUG00000015939 6 retrocopies
Oryctolagus cuniculus ENSOCUG000000220151 retrocopy
Pongo abelii ENSPPYG000000034375 retrocopies
Pan troglodytes ENSPTRG000000034215 retrocopies
Rattus norvegicus ENSRNOG0000001300917 retrocopies
Sorex araneus ENSSARG000000012241 retrocopy
Sarcophilus harrisii ENSSHAG000000157761 retrocopy
Sus scrofa ENSSSCG000000133661 retrocopy
Tarsius syrichta ENSTSYG000000080624 retrocopies
Tursiops truncatus ENSTTRG000000137562 retrocopies
Vicugna pacos ENSVPAG000000102155 retrocopies



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