RetrogeneDB ID:

retro_rnor_947

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:13:4029874..4030717(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Vdac1
Ensembl ID:ENSRNOG00000006375
Aliases:None
Description:Voltage-dependent anion-selective channel protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2L0]


Retrocopy-Parental alignment summary:






>retro_rnor_947
ATGGCTGTGCTTCCCGCATATGCTGATCTTGGCAAGTCCGCCAGGGATGTCTTCACCAAGGGCTACGGCTTTGGCTTAAT
AAAATTTGATTTGAAAACGAAGTCTGAGAATGGATTGGAATTTACTAGCTCAGGTTCTGCCAACACGGAGACCACCAAAG
TGAACGGCAGTCTGGAAACCAAGTACAGATGGACTGAGTATGGGCTGACGTTTATTGAGAAGTGGAACACAGACAACACC
CTGGACACTGAGATCTCAGTGGAAGGCCAGCTTGGTCATGGACTGAAGCTGACTTTTGATTCATTTTTCTCGCCTAATAC
TGGGGAAAAAATGCTTAAATCAAGACAGGGTACAAGGGGAGCATATAAACCTGGGCTGTGGTGTGGACTTTGACGTAGCT
GGGCCCTCAATCCGGTGCGTTCTGCTGCTTGGCTATGAGGGTTGGCTGGCGGGCTACCAGATGAATTTTGAGACCTCGAA
GTCCCGAGTGACCCAGAGCAACTTTGCAGTTGGCAACAAGACGGATGAATTCCAGCTTCATACTAATGTGAATGATGGGA
CGTAGGTTGGTGGCTCCATTTACCAGAAGGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCGCCTGGACCACAGGAAAC
AGTAACACTCGCTTTGGAATAGCAGCCAACTATCAGGTGGCGCTGATGCTTGCTTTTCGGCCAAAGTGAACAACCCCAGT
CTAATTGGCTTAGGATACACTCAGACCCTAAAACCAGGTACCAAACTGATGCTGTCAGCCCTGCCGAATGGCAAGAATGT
CAATGGGGGCGGCCACAAGCTTGGTTTAGGACTGGAATTTCAA

ORF - retro_rnor_947 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.07 %
Parental protein coverage: 99.65 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVNGSLETKYRWTEYGLT
MAV.P.YADLGKSARDVFTKGYGFGLIK.DLKTKSENGLEFTSSGSANTETTKVNGSLETKYRWTEYGLT
RetrocopyMAVLPAYADLGKSARDVFTKGYGFGLIKFDLKTKSENGLEFTSSGSANTETTKVNGSLETKYRWTEYGLT
ParentalFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGK-KNAKIKTGYK-REHINLGCDVDFDIAGPSI
F.EKWNTDNTL.TEI.VE.QL..GLKLTFDS.FSPNTG..KNA.IKTGYK..EHINLGC.VDFD.AGPSI
RetrocopyFIEKWNTDNTLDTEISVEGQLGHGLKLTFDSFFSPNTGE<KNA*IKTGYK<GEHINLGCGVDFDVAGPSI
ParentalRGALVLGYEGWLAGYQMNFETSKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNL
R..L.LGYEGWLAGYQMNFETSKSRVTQSNFAVG.KTDEFQLHTNVNDGT..GGSIYQKVNKKLETAVNL
RetrocopyRCVLLLGYEGWLAGYQMNFETSKSRVTQSNFAVGNKTDEFQLHTNVNDGT*VGGSIYQKVNKKLETAVNL
ParentalAWTAGNSNTRFGIAAKYQV-DPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGL
AWT.GNSNTRFGIAA.YQV...DACFSAKVNN.SLIGLGYTQTLKPG.KL.LSAL..GKNVN.GGHKLGL
RetrocopyAWTTGNSNTRFGIAANYQV<GADACFSAKVNNPSLIGLGYTQTLKPGTKLMLSALPNGKNVNGGGHKLGL
ParentalGLEFQ
GLEFQ
RetrocopyGLEFQ

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






RNA-Seq - click to see more details

(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 154 .43 RPM
SRP017611_kidney 0 .07 RPM 345 .21 RPM
SRP017611_liver 0 .00 RPM 73 .63 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_947 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_947 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_947 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 31 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009851 retrocopy
retro_cfam_1728,
Choloepus hoffmanni ENSCHOG000000056316 retrocopies
retro_chof_1774, retro_chof_2420, retro_chof_813, retro_chof_858, retro_chof_866, retro_chof_99,
Callithrix jacchus ENSCJAG000000135568 retrocopies
retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Cavia porcellus ENSCPOG000000238402 retrocopies
retro_cpor_1061, retro_cpor_699,
Dasypus novemcinctus ENSDNOG000000026805 retrocopies
retro_dnov_1367, retro_dnov_2117, retro_dnov_271, retro_dnov_30, retro_dnov_90,
Dipodomys ordii ENSDORG000000007141 retrocopy
retro_dord_636,
Equus caballus ENSECAG000000123652 retrocopies
retro_ecab_831, retro_ecab_832,
Felis catus ENSFCAG000000084211 retrocopy
retro_fcat_1592,
Homo sapiens ENSG0000021358513 retrocopies
retro_hsap_1119, retro_hsap_1250, retro_hsap_2250, retro_hsap_2805, retro_hsap_308, retro_hsap_3527, retro_hsap_4287, retro_hsap_458, retro_hsap_4721, retro_hsap_4831, retro_hsap_4872, retro_hsap_4930, retro_hsap_847,
Gorilla gorilla ENSGGOG000000108803 retrocopies
retro_ggor_693, retro_ggor_875, retro_ggor_981,
Loxodonta africana ENSLAFG000000288181 retrocopy
retro_lafr_161,
Macaca mulatta ENSMMUG000000162356 retrocopies
retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Monodelphis domestica ENSMODG000000141571 retrocopy
retro_mdom_1120,
Mustela putorius furoENSMPUG000000102201 retrocopy
retro_mputfur_83,
Mus musculus ENSMUSG000000204023 retrocopies
retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Nomascus leucogenys ENSNLEG0000000802311 retrocopies
retro_nleu_1044, retro_nleu_1318, retro_nleu_1561, retro_nleu_189, retro_nleu_1991, retro_nleu_2707, retro_nleu_3019, retro_nleu_433, retro_nleu_492, retro_nleu_873, retro_nleu_880,
Oryctolagus cuniculus ENSOCUG000000093693 retrocopies
retro_ocun_1253, retro_ocun_1428, retro_ocun_583,
Otolemur garnettii ENSOGAG000000307422 retrocopies
retro_ogar_1197, retro_ogar_2876,
Ochotona princeps ENSOPRG000000066052 retrocopies
retro_opri_397, retro_opri_467,
Pongo abelii ENSPPYG000000157816 retrocopies
retro_pabe_1042, retro_pabe_1733, retro_pabe_273, retro_pabe_2913, retro_pabe_3756, retro_pabe_700,
Pan troglodytes ENSPTRG0000001723512 retrocopies
retro_ptro_1593, retro_ptro_1900, retro_ptro_249, retro_ptro_2905, retro_ptro_3138, retro_ptro_3215, retro_ptro_3246, retro_ptro_345, retro_ptro_588, retro_ptro_682, retro_ptro_84, retro_ptro_861,
Rattus norvegicus ENSRNOG00000006375 8 retrocopies
retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947 ,
Rattus norvegicus ENSRNOG000000135051 retrocopy
retro_rnor_2652,
Rattus norvegicus ENSRNOG000000192771 retrocopy
retro_rnor_1596,
Sorex araneus ENSSARG000000082216 retrocopies
retro_sara_115, retro_sara_327, retro_sara_355, retro_sara_533, retro_sara_668, retro_sara_702,
Sus scrofa ENSSSCG000000142962 retrocopies
retro_sscr_346, retro_sscr_801,
Ictidomys tridecemlineatus ENSSTOG000000077643 retrocopies
retro_itri_1137, retro_itri_1506, retro_itri_693,
Tupaia belangeri ENSTBEG000000038524 retrocopies
retro_tbel_1282, retro_tbel_2613, retro_tbel_3818, retro_tbel_4546,
Tarsius syrichta ENSTSYG000000073461 retrocopy
retro_tsyr_161,
Tursiops truncatus ENSTTRG000000168562 retrocopies
retro_ttru_1347, retro_ttru_752,
Vicugna pacos ENSVPAG000000104481 retrocopy
retro_vpac_38,


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