RetrogeneDB ID:

retro_cjac_3315

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:73183313..73184122(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000019424
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSCJAG00000002392
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]


Retrocopy-Parental alignment summary:






>retro_cjac_3315
ATGTTCTCGTCCGTGGGGCACGTGGTGCACTTGGAGCAGGCGAACCCCTTCAACACGCCTCATCTGCAGCTGGTGCACGA
TGGCCTCGCGGACCTCCGCAGCAGAGCCCTCCAGGGCCCACAGGGCAGCCCCTCCGCCCTCACAACCTGGCAGCCGCTGC
CGTGGAAGAGTACAGTTGTGAATTTGGCTCTGCGAAGTATTATGCACTGCGTGGCTTCGGTGGGGTCTTAAGTTGTGGTC
TGACACACACTGCTGTCGTTCCCCTGGATTTAGTGAAATGTCGTATGCAGGTGGACCCCCAAAAGTACAAGGACATATTT
AACGGATTCTCAGTTACACTTACGGGGCATGGTGTTCGTGGGTTGGCCAAAGGATGGGCTCCGACATTCATTGGCTACTC
CCTGCAAGGGCTCTGTAAGTTTGGCTTTTATGAAGTCTTTAAAGTCTTGTATAGCAACATGCTTGGAGAGGAGAATACTC
ATCTCTGGCGCACATCATTATATTTGGCTGCCTCTGCCAGTGCTGAATTCTTTGCTGACACTGCCCTGGCGCCTATGGAA
GCTGCTAAGGTTCGAATTCAAACCCAACCAGGTTATGCCAACACTTTGATGGGTGCAGCTCCCAAAATGTATAAGGAAGA
AGGCCTAAGAGCATTCAACAACGGGGTTGCTCCTCTCTGGATGAGACAGCTACCATACACCATGATGAACTTTGCCTGCT
TTGAACGTACTGTTGAAGCACTATACAAGTTTATGGTTCCCAAGACCGGCAGTGAATGTTCAAAGCCAGAGCAGCTGGTT
GTAACATTT

ORF - retro_cjac_3315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.82 %
Parental protein coverage: 73.68 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMFSS---VAHLARANPFNAPHMQLVHDGFADLRS-SPPGP-TGQPRRPRNLAAAAVEEYSCEFGSAKYYA
MFSS...V.HL..ANPFN.PH.QLVHDG.ADLRS....GP.TGQP.RP.NLAAAAVEEYSCEFGSAKYYA
RetrocopyMFSSVGHVVHLEQANPFNTPHLQLVHDGLADLRSRALQGP<TGQPLRPHNLAAAAVEEYSCEFGSAKYYA
ParentalLCGFGGVLSCGLTHTAVVPLDLVKCRMQVDPQKYKGIFNGFSVTLKEDGVRGLAKGWAPTFIGYSLQGLC
L.GFGGVLSCGLTHTAVVPLDLVKCRMQVDPQKYK.IFNGFSVTL...GVRGLAKGWAPTFIGYSLQGLC
RetrocopyLRGFGGVLSCGLTHTAVVPLDLVKCRMQVDPQKYKDIFNGFSVTLTGHGVRGLAKGWAPTFIGYSLQGLC
ParentalKFGFYEVFKVLYSNMLGEENTYLWRTSLYLAASASAEFFADIALAPMEAAKVRIQTQPGYANTLRDAAPK
KFGFYEVFKVLYSNMLGEENT.LWRTSLYLAASASAEFFAD.ALAPMEAAKVRIQTQPGYANTL..AAPK
RetrocopyKFGFYEVFKVLYSNMLGEENTHLWRTSLYLAASASAEFFADTALAPMEAAKVRIQTQPGYANTLMGAAPK
ParentalMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSECSKPEQLVVTF
MYKEEGL.AF..GVAPLWMRQ.PYTMM.FACFERTVEALYKF.VPK..SECSKPEQLVVTF
RetrocopyMYKEEGLRAFNNGVAPLWMRQLPYTMMNFACFERTVEALYKFMVPKTGSECSKPEQLVVTF

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
SRP051959_colon 0 .02 RPM 133 .52 RPM
SRP051959_heart 0 .04 RPM 235 .18 RPM
SRP051959_kidney 0 .07 RPM 140 .02 RPM
SRP051959_liver 0 .02 RPM 96 .50 RPM
SRP051959_lung 0 .02 RPM 62 .63 RPM
SRP051959_lymph_node 0 .05 RPM 60 .68 RPM
SRP051959_skeletal_muscle 0 .11 RPM 274 .96 RPM
SRP051959_spleen 0 .00 RPM 74 .26 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3315 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3315 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3315 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000132321 retrocopy
retro_acar_35,
Bos taurus ENSBTAG000000128901 retrocopy
retro_btau_172,
Canis familiaris ENSCAFG000000065451 retrocopy
retro_cfam_880,
Callithrix jacchus ENSCJAG00000002392 2 retrocopies
retro_cjac_3315 , retro_cjac_812,
Dipodomys ordii ENSDORG000000114311 retrocopy
retro_dord_321,
Equus caballus ENSECAG000000151351 retrocopy
retro_ecab_481,
Echinops telfairi ENSETEG000000126781 retrocopy
retro_etel_1748,
Homo sapiens ENSG000000754151 retrocopy
retro_hsap_392,
Gorilla gorilla ENSGGOG000000158861 retrocopy
retro_ggor_394,
Latimeria chalumnae ENSLACG000000070241 retrocopy
retro_lcha_4,
Macropus eugenii ENSMEUG000000165932 retrocopies
retro_meug_405, retro_meug_658,
Microcebus murinus ENSMICG000000035201 retrocopy
retro_mmur_298,
Myotis lucifugus ENSMLUG000000083301 retrocopy
retro_mluc_1184,
Macaca mulatta ENSMMUG000000230361 retrocopy
retro_mmul_496,
Monodelphis domestica ENSMODG000000077172 retrocopies
retro_mdom_2026, retro_mdom_293,
Mus musculus ENSMUSG000000619041 retrocopy
retro_mmus_1959,
Nomascus leucogenys ENSNLEG000000059731 retrocopy
retro_nleu_2402,
Oryctolagus cuniculus ENSOCUG000000118471 retrocopy
retro_ocun_390,
Otolemur garnettii ENSOGAG000000122222 retrocopies
retro_ogar_1816, retro_ogar_2052,
Pongo abelii ENSPPYG000000048581 retrocopy
retro_pabe_1768,
Pan troglodytes ENSPTRG000000053331 retrocopy
retro_ptro_302,
Pteropus vampyrus ENSPVAG000000058901 retrocopy
retro_pvam_212,
Sorex araneus ENSSARG000000011491 retrocopy
retro_sara_262,
Ictidomys tridecemlineatus ENSSTOG000000276332 retrocopies
retro_itri_485, retro_itri_90,
Tupaia belangeri ENSTBEG000000145481 retrocopy
retro_tbel_1792,
Tursiops truncatus ENSTTRG000000047391 retrocopy
retro_ttru_692,
Vicugna pacos ENSVPAG000000047041 retrocopy
retro_vpac_455,




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