RetrogeneDB ID:

retro_rnor_254

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:149406449..149406872(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000004700
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Nxt2
Ensembl ID:ENSRNOG00000019168
Aliases:Nxt2, RGD1560204
Description:NTF2-related export protein 2 [Source:UniProtKB/Swiss-Prot;Acc:B2GV77]


Retrocopy-Parental alignment summary:






>retro_rnor_254
ATGGCATCAGTAGATTTCAAGACCTATGTGGACCAGGCCTGCAGAGCTGCAGAGGAATTTGTCAACGTCTACTACACTAC
TATGGATAATCGGCGGCGGCTGCTGTCTCGCCTGTACATGGGCACGGCCACTTTAGTATGGAATGGAAATGCCGTTTCGG
GACAAGAATCCTTGAGTGAGTTTTTTGAGATGTTGCCTTCCAGTGAGTTCCAAATCAACGTGGTAGACTGCCAGCCTGTT
CATGATGAAGCTACGCCAAGCCAGACCACGGTCCTTGTGGTCATCTGTGGAACAGTGAAATTTGAGGGCAACAAACAGCG
GGACTTCAACCAGAACTTCATCCTGACTGCTCAGGCGTCACCCAGTAACACAGTGTGGAAGATAGCGAGTGACTGCTTCC
GCTTCCAGGACTGGGCCAGCTAG

ORF - retro_rnor_254 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.64 %
Parental protein coverage: 97.18 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAVDFKMYVDQACRAAEEFVNIYYETMDKRRHALVRLYLDKATLIWNGNVVTGLEALANFFEMLPSSEFQI
.VDFK.YVDQACRAAEEFVN.YY.TMD.RR..L.RLY...ATL.WNGN.V.G.E.L..FFEMLPSSEFQI
RetrocopySVDFKTYVDQACRAAEEFVNVYYTTMDNRRRLLSRLYMGTATLVWNGNAVSGQESLSEFFEMLPSSEFQI
ParentalNMLDCQPVHEQATQYQTTVLVVTSGVVKFDGNKQHFFNQNFLLTAQSTPNSTVWKIASDCFRFQDWAS
N..DCQPVH..AT..QTTVLVV..G.VKF.GNKQ..FNQNF.LTAQ..P..TVWKIASDCFRFQDWAS
RetrocopyNVVDCQPVHDEATPSQTTVLVVICGTVKFEGNKQRDFNQNFILTAQASPSNTVWKIASDCFRFQDWAS

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 2 .01 RPM 4 .17 RPM
SRP017611_kidney 3 .77 RPM 9 .14 RPM
SRP017611_liver 1 .61 RPM 6 .52 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_254 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_254 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_254 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_80
Gorilla gorilla retro_ggor_67
Pongo abelii retro_pabe_101
Macaca mulatta retro_mmul_140
Callithrix jacchus retro_cjac_98
Mus musculus retro_mmus_12
Oryctolagus cuniculus retro_ocun_210
Bos taurus retro_btau_118
Sus scrofa retro_sscr_8
Canis familiaris retro_cfam_1137
Parental genes homology:
Parental genes homology involve 28 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000179991 retrocopy
retro_amel_59,
Bos taurus ENSBTAG000000207391 retrocopy
retro_btau_118,
Canis familiaris ENSCAFG000000285741 retrocopy
retro_cfam_1137,
Callithrix jacchus ENSCJAG000000073691 retrocopy
retro_cjac_98,
Cavia porcellus ENSCPOG000000033101 retrocopy
retro_cpor_29,
Dipodomys ordii ENSDORG000000107141 retrocopy
retro_dord_2,
Echinops telfairi ENSETEG000000080022 retrocopies
retro_etel_1926, retro_etel_1979,
Felis catus ENSFCAG000000022401 retrocopy
retro_fcat_20,
Homo sapiens ENSG000001018881 retrocopy
retro_hsap_80,
Gorilla gorilla ENSGGOG000000135931 retrocopy
retro_ggor_67,
Loxodonta africana ENSLAFG000000071161 retrocopy
retro_lafr_124,
Microcebus murinus ENSMICG000000145113 retrocopies
retro_mmur_149, retro_mmur_1531, retro_mmur_25,
Myotis lucifugus ENSMLUG000000006313 retrocopies
retro_mluc_1513, retro_mluc_160, retro_mluc_473,
Macaca mulatta ENSMMUG000000132041 retrocopy
retro_mmul_140,
Monodelphis domestica ENSMODG000000213431 retrocopy
retro_mdom_1611,