RetrogeneDB ID:

retro_ecab_481

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:2:5978412..5979278(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000018715
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A3
Ensembl ID:ENSECAG00000015135
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]


Retrocopy-Parental alignment summary:






>retro_ecab_481
GGCGGCATGCTGAGCTGCCGCTGACGCACACGGCCATCGTGCCCTGGACCTGGTCAAGTGCCGCATGCAGGTGGACCCCG
GCAAGTACTCAGGGCATCCTCAGCGGCTTCTGGCGTGACGCTGCGGGACGAACGGGCTGCGCGACCTGGCCCGACGACTG
AGACCCCGAACTTTCCTGGGCTACTCGCTGCAGAGACTCTTCAAGTACGGCCTGTACGAGATCTTCAAAGTACACTACGC
GGAGCGCCTGAGCCCGAGAGGGGCTACGCCTGGAGGACCGGCCTGTACCTGACCGCCTCGGCCAGCGCCGAGTTCTTCGC
CCGACGTGGCGCTGGCCCCCATGGAGGCGGTGAAGGTGCGCATCCAGACGCAGCCCGGCTTCGCCCCGCACGCTGCGGGC
CGCCGCCCCGCGCATGTACGGCGAGGAGGGCCTGCGGGCCTTCTACAAGGGCGTGGCGCCGCTCTGGCTGCGGCAGATCC
CCTACACCATGATGAAGTTCGCCTGCTTCGAGCGCACGGTGGAGGCGCTCTACACCTACGTGGTGCCCAAGCCCCAGAGC
CAGTGCTCCAAGGCCGAGCAGCTGGCCGTGACCTTCGTGGCCGGCTACATCGCCGGCGTCTTCTGTGCCGTCGTGTCCCA
CCCGGCCGATTCCGTCGTGTCCGTTTTGAACAAGGAGAAAGGCAGCACGGCCTTCGGGGTTCTCCGCAGACTGGGGTTCT
GGGGCGTGTGGAAGGGCCTGTTCGCCCGGATCATCATGATCGGCACCCTGACTGCGCTGCAGTGGTTCATCTACGACTCG
GTCAAGGTCTATTTCAAGCTGCCTCGCCCTCCGGTCCCGCAACCGCCCGAATCCCTGAAAGAGCAG

ORF - retro_ecab_481 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.35 %
Parental protein coverage: 80.17 %
Number of stop codons detected: 0
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalGGVLSCG-LTHTAVVP-LDLVKCRMQVDPQKY-KGIFNGF-SVTLKED-GVRGLAKGWAP-TFIGYSLQG
GG.LSC..LTHTA.VP.LDLVKCRMQVDP.KY..GI..GF..VTL....G.R.LA....P.TF.GYSLQ.
RetrocopyGGMLSCR<LTHTAIVP<LDLVKCRMQVDPGKY>QGILSGF>GVTLRDE>GLRDLARRLRPRTFLGYSLQR
ParentalLCKFGFYEVFKVLYSNVLGE-ENAYVWRTSLYLAASASAEFFA-DIALAPMEATKVRIQTQPGYA-NTLR
L.K.G.YE.FKV.Y...L...E..Y.WRT.LYL.ASASAEFFA.D.ALAPMEA.KVRIQTQPG.A..TLR
RetrocopyLFKYGLYEIFKVHYAERLSP<ERGYAWRTGLYLTASASAEFFA>DVALAPMEAVKVRIQTQPGFA>RTLR
ParentalDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSECSKPEQLVVTFVAGY
.AAP.MY.EEGL.AFYKGVAPLW.RQIPYTMMKFACFERTVEALY..VVPKP.S.CSK.EQL.VTFVAGY
RetrocopyAAAPRMYGEEGLRAFYKGVAPLWLRQIPYTMMKFACFERTVEALYTYVVPKPQSQCSKAEQLAVTFVAGY
ParentalIAGVFCAIVSHPADSVVSVLNKEKGSSASQVLQRLGFKGVWKGLFARIIMIGTLTALQWFIYDSVKVYFR
IAGVFCA.VSHPADSVVSVLNKEKGS.A..VL.RLGF.GVWKGLFARIIMIGTLTALQWFIYDSVKVYF.
RetrocopyIAGVFCAVVSHPADSVVSVLNKEKGSTAFGVLRRLGFWGVWKGLFARIIMIGTLTALQWFIYDSVKVYFK
ParentalLPRPPPPEMPESLKKK
LPRPP.P..PESLK..
RetrocopyLPRPPVPQPPESLKEQ

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
SRP021940_articular_cartilage 0 .00 RPM 388 .12 RPM
SRP021940_cerebellum 0 .00 RPM 421 .85 RPM
SRP021940_embryo 0 .00 RPM 225 .47 RPM
SRP021940_placental_villous 0 .14 RPM 394 .08 RPM
SRP021940_synovial_membrane 0 .03 RPM 216 .10 RPM
SRP021940_testis 31 .01 RPM 93 .23 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_481 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_481 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_481 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_392
Pan troglodytes retro_ptro_302
Gorilla gorilla retro_ggor_394
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 ENSCJAG000000023922 retrocopies
retro_cjac_3315, retro_cjac_812,
Dipodomys ordii ENSDORG000000114311 retrocopy
retro_dord_321,
Equus caballus ENSECAG00000015135 1 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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