RetrogeneDB ID:

retro_rnor_1934

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:156315382..156316480(-)
Located in intron of:ENSRNOG00000016352
Retrocopy
information
Ensembl ID:ENSRNOG00000031275
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Sms
Ensembl ID:ENSRNOG00000007688
Aliases:None
Description:spermine synthase [Source:RefSeq peptide;Acc:NP_001029071]


Retrocopy-Parental alignment summary:






>retro_rnor_1934
ATGGCAGCAGCAAGGCACAGCACGCTCGACTTCACGCTCGGCGCCAAAGCTGATGGTGAGGCCATTCTGAAAGGCCTTCA
GTCCATCTTTCAGGAGCAGGGGATGGCAGAGTCGGTGCACACCTGGCAGGACCATGGGTATTTAGCAACCTACACGAACA
AGAATGGCAGCTTTGCCAATTTGAGAATTTATCCACATGGATTGGTGTTGCTGGACCTTCAGAGTTACGACAGTGATGTG
CAAGGCAAACAAGAAACTGACAGCCTTTTGAATAAAATAGAAGAAAAAATGAAAGAATTGAGTCAAGACAGTACTGGTCG
GGTGAAGCGACTACCACCCATAGTTCGAGGAGGGGCCATTGACAGATACTGGCCTACTGCTGACGGGCGCCTGGTTGAGT
ATGACATAGATGAAGTGGTGTATGACGAAGACTCGCCTTATCAGAACATTAAAATTCTTCACTCAAAACAGTTTGGGAAT
ATTCTCATCCTCAGCGGGGATGTTAATTTGGCAGAGAGTGACTTGGCATATACCAGGGCCATCATGGGCAATGGTAAAGA
AGACTACACTGGCAAAGATGTACTGATTCTGGGAGGCGGCGATGGAGGCATATTATGTGAAATTGTCAAACTGAAACCAA
AGATGGTCACTATGGTAGAGATTGACCAGATGGTAATTGATGGATGTAAGAAATACATGCGCAGAACATGTGGAGATGTC
TTAGACAATCTTAAAGGAGATTGCTATCAGGTTCTTATAGAAGACTGTATCCCAGTACTGAAGAGGTACGCCAAAGAAGG
GAGAGAGTTTGATTATGTGATTAATGATTTGACAGCTGTCCCTATCTCTACATCTCCAGAAGAAGATTCCACATGGGAGT
TTCTCAGACTGATTCTTGACCTGTCAATGAAGGTTCTGAAACAGGATGGAAAATATTTCACACAGGGGAACTGTGTCAAC
TTGACTGAAGCCCTGTCCCTCTATGAAGAACAGCTGGGGCGCCTGTATTGTCCTGTGGAATTCTCAAAAGAGATTGTCTG
TGTCCCTTCATACTTGGAATTGTGGGTATTTTACACTGTTTGGAAGAAAGCTAAGCCT

ORF - retro_rnor_1934 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.73 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAAARHSTLDFTLGAKADGEAILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVL
MAAARHSTLDFTLGAKADGEAILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVL
RetrocopyMAAARHSTLDFTLGAKADGEAILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVL
ParentalLDLQSYDSDVQGKQETDCLLNKIEEKMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVV
LDLQSYDSDVQGKQETD.LLNKIEEKMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVV
RetrocopyLDLQSYDSDVQGKQETDSLLNKIEEKMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVV
ParentalYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGNGKEDYTGKDVLILGGGDGGILCEIVK
YDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGNGKEDYTGKDVLILGGGDGGILCEIVK
RetrocopyYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGNGKEDYTGKDVLILGGGDGGILCEIVK
ParentalLKPKMVTMVEIDQMVIDGCKKYMRRTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAV
LKPKMVTMVEIDQMVIDGCKKYMRRTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAV
RetrocopyLKPKMVTMVEIDQMVIDGCKKYMRRTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAV
ParentalPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPS
PISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPS
RetrocopyPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPS
ParentalYLELWVFYTVWKKAKP
YLELWVFYTVWKKAKP
RetrocopyYLELWVFYTVWKKAKP

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 .65 RPM 32 .64 RPM
SRP017611_kidney 0 .49 RPM 11 .86 RPM
SRP017611_liver 0 .07 RPM 2 .15 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_1934 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1934 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1934 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000183821 retrocopy
retro_btau_1412,
Canis familiaris ENSCAFG000000132843 retrocopies
retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus ENSCJAG000000339331 retrocopy
retro_cjac_518,
Cavia porcellus ENSCPOG000000061762 retrocopies
retro_cpor_729, retro_cpor_889,
Echinops telfairi ENSETEG000000100982 retrocopies
retro_etel_1066, retro_etel_1540,
Homo sapiens ENSG000001021725 retrocopies
retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla ENSGGOG000000031233 retrocopies
retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus ENSMICG000000001923 retrocopies
retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus ENSMLUG000000131853 retrocopies
retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta ENSMMUG000000203922 retrocopies
retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica ENSMODG000000078971 retrocopy
retro_mdom_412,
Mus musculus ENSMUSG000000717086 retrocopies
retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys ENSNLEG000000099554 retrocopies
retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus ENSOCUG000000060162 retrocopies
retro_ocun_1458, retro_ocun_1918,
Pongo abelii ENSPPYG000000201824 retrocopies
retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus ENSPVAG000000167851 retrocopy
retro_pvam_524,
Rattus norvegicus ENSRNOG00000007688 2 retrocopies
retro_rnor_1934 , retro_rnor_938,
Tupaia belangeri ENSTBEG000000121093 retrocopies
retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos ENSVPAG000000075431 retrocopy
retro_vpac_50,


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