RetrogeneDB ID:

retro_ecab_76

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:2:61593146..61594298(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002223
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:eca-mir-492-1
Ensembl ID:ENSECAG00000014086
Aliases:None
Description:eca-mir-492-1 [Source:miRBase;Acc:MI0012676]


Retrocopy-Parental alignment summary:






>retro_ecab_76
ATGACTACCTACAGCTATCGCCAGTCCTCGGCCACCTCGTCCTTCGGGGGCCTGGGCAGTGGCTCCCTGCGCTTCGGGGC
CGGAGGCACCATCCGCGCGCCCAGCATCCACGGGGGCTCGGGCGGCCGCGGCGTGTCGGTGTCCTCTGCCAGCTTCGTGA
CCTCGTCCTCCTCCGGGAGCTACGGCGGTGGCTATGCGGGCACCCTGGCCGGGTCCGACGGGCTGCCGGCGGGCAACGAG
AAGGAGACCATGCAGAACCTCAACGACCGCCTGGCCTCCTACCTGGACATGGTGCGCGCCCTGGAGCAGGCCAACGGCGA
CCTGGAGGTGAAGATCCGCGACTGGTACCTGAAGCAGGGGCCCGGGCCCGCCCGCGACTACAGCCACTACTTCAAGACCA
TCGAGGAGCTGCGGGACAAGATTCTTGGGGCCACCATTGAGAACTCCAAGATTGTTCTGCAGATCGACAATGCCCGTCTG
GCTGCAGACGATTTCCGAACCAAGTTCGAGACTGAGCAGGCTCTGCGCTTGAGTGTGGAGGCCGACATCAATGGCCTGCG
CAGGGTGCTAGACGAGCTGACCCTGGCCAGGACTGACCTGAAGATGCAGATCGAAGGCCTGAAGGAGGAGCTGGCCTACC
TGAAGAAGAACCACGAGGAGGAAATCAGTGTCTTGAGGGGCCAGGTCACTGTGGAGGTGGATTCCGCTCCAGGCATTGAC
CTAGCCAAGATCCTGAGCGACATGAGAAGCCAATATGAGGTCATGGCTGAGAAGAACAGGAAGGATGCTGAAGCCTGGTT
CACCACCAAGACTGAGGAGCTGAACCGGGAGGTCGCTGGCCACACGGAGCAGCTGCAGATTAACAAGACGGAGATCACCG
ACCTGCGGCGCACCCTCCAGGGCCTGGAGATCGAGCTGCAGTCTCAGCTCAGCATGAAAGCCGCCCTGGAAGGCACGCTG
GCGGAAACGGAGGCTCGCTTCGGAGCTCAGCTGGCACAGATCCAGGCGCTGATCAGTAGCATCGAAGCCCAGCTGAGTGA
CGTGCGTGCTGACACCGAGCGGCAGAACCAGGAGTACCAGCTGCTCCTGGACGTCAAGACTCGGGTGGAGCAGGAGATCG
CCACCTACCGAAGCCTGCTGGAGGCCCAGGAC

ORF - retro_ecab_76 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.16 %
Parental protein coverage: 98.48 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMTSYSYRQSSATSSFGGLGSGSLRFGAGGNFRAPSIHGGSGGRGVSVSSARFVTSSSSGSYGGGYAGTLA
MT.YSYRQSSATSSFGGLGSGSLRFGAGG..RAPSIHGGSGGRGVSVSSA.FVTSSSSGSYGGGYAGTLA
RetrocopyMTTYSYRQSSATSSFGGLGSGSLRFGAGGTIRAPSIHGGSGGRGVSVSSASFVTSSSSGSYGGGYAGTLA
ParentalGSDGLPAGNEKETMQNLNDRLASYLDKVRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK
GSDGLPAGNEKETMQNLNDRLASYLD.VRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK
RetrocopyGSDGLPAGNEKETMQNLNDRLASYLDMVRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK
ParentalILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLEMQIEGLKEE
ILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDL.MQIEGLKEE
RetrocopyILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLKMQIEGLKEE
ParentalLAYLKKNHEEEISVLRGQVGGQVTVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR
LAYLKKNHEEEISVLRGQV....TVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR
RetrocopyLAYLKKNHEEEISVLRGQV----TVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR
ParentalEVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS
EVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS
RetrocopyEVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS
ParentalDVRADTERQNQEYQLLLDVKTRLEQEIATYRSLLEAQD
DVRADTERQNQEYQLLLDVKTR.EQEIATYRSLLEAQD
RetrocopyDVRADTERQNQEYQLLLDVKTRVEQEIATYRSLLEAQD

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 0 .00 RPM
SRP021940_cerebellum 0 .00 RPM 0 .00 RPM
SRP021940_embryo 0 .03 RPM 3 .99 RPM
SRP021940_placental_villous 0 .19 RPM 15 .06 RPM
SRP021940_synovial_membrane 0 .00 RPM 0 .08 RPM
SRP021940_testis 0 .00 RPM 0 .51 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_76 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_76 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_76 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000297569 retrocopies
retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus ENSECAG00000014086 2 retrocopies
retro_ecab_76 , retro_ecab_931,
Echinops telfairi ENSETEG000000078816 retrocopies
retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens ENSG000001713453 retrocopies
retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla ENSGGOG000000169013 retrocopies
retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii ENSMEUG000000161583 retrocopies
retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta ENSMMUG000000186534 retrocopies
retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys ENSNLEG000000107873 retrocopies
retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus ENSOCUG000000161321 retrocopy
retro_ocun_1884,
Otolemur garnettii ENSOGAG000000243061 retrocopy
retro_ogar_1301,
Ochotona princeps ENSOPRG000000079082 retrocopies
retro_opri_337, retro_opri_673,
Pongo abelii ENSPPYG000000084163 retrocopies
retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes ENSPTRG000000091683 retrocopies
retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus ENSSTOG000000144032 retrocopies
retro_itri_1514, retro_itri_697,


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