RetrogeneDB ID:

retro_ecab_96

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:6:74501158..74501890(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000006594
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000013915
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ecab_96
ATGGCGGTGCAAATTTCCAAGAAGAGGCAGTTTGTAGCTCACGGCATCTTCAAAGCTGAACTGAACGAGTTCCTCACTCG
GGAGCTGGCTGAAGATGGCTACTCTGGAGTTGAGGTCCGGGTTACACCCACCAGGACGGAAATCATCATCTTGGCCACCA
GGACGCAGAATGTTCTTGGTGAGAAGGGCCGGCGGATCCGGGAATTGACCGCTGTGGTTCAGAAGAGATTTGGCTTCCCT
GAGGGCAGTGTAGAGCTGTATGCTGAAAAGGTGGCCAAGAGGGGTCTGTGTGCCATTGCCCAGGCAGAGTCTCTGCGCTA
CAAACTCCTGGGAGGCCTTGCTGTGCGGAGGGCCTGCTATGGTGTGCTGCGGTTCACCATGGAGAGTGGGGCCAAAGGCT
GCGAGGTCGTGGTGTCTGGGAAACTCCGAGGACAGAGGGCTAAATCCATGAAGTTTGTGGACGGCCTGATGATCCACAGT
GGGGACCCTGTCAACTACTATGTGGACACTGCTGTGTGCCATGTACTGCTTAGACAGGGTGTGCTGGGCATCAAAGTGAA
GATCATGCTGCCTTGGGACCCAAGTGGTAAGATTGGCCCTAAGAAGCCGCTGCCTGACCACGTGAGCATCGTGGAACCCA
AAGATGAGATACTGCCCACCACCCCCATCTCAGAACAGAAGGGTGGGAAGCCAGAGCCGCCTGCCATGCCCCAGCCAGTA
CCCATGGCATAA

ORF - retro_ecab_96 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELT
MAVQISKKR.FVA.GIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELT
RetrocopyMAVQISKKRQFVAHGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELT
ParentalAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSG
AVVQKRFGFPEGSVELYAEKVA.RGLCAIAQAESLRYKLLGGLAVRRACYGVLRF.MESGAKGCEVVVSG
RetrocopyAVVQKRFGFPEGSVELYAEKVAKRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFTMESGAKGCEVVVSG
ParentalKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPDHVSI
KLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAV.HVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPDHVSI
RetrocopyKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVCHVLLRQGVLGIKVKIMLPWDPSGKIGPKKPLPDHVSI
ParentalVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA
VEPKDEILPTTPISEQKGGKPEPPAMPQPVP.A
RetrocopyVEPKDEILPTTPISEQKGGKPEPPAMPQPVPMA

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 509 .19 RPM
SRP021940_cerebellum 0 .00 RPM 204 .67 RPM
SRP021940_embryo 4 .83 RPM 329 .43 RPM
SRP021940_placental_villous 1 .20 RPM 244 .93 RPM
SRP021940_synovial_membrane 2 .53 RPM 401 .60 RPM
SRP021940_testis 0 .90 RPM 127 .69 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_96 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_96 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_96 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 30 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170512 retrocopies
retro_amel_1483, retro_amel_465,
Bos taurus ENSBTAG000000056204 retrocopies
retro_btau_1626, retro_btau_425, retro_btau_909, retro_btau_924,
Canis familiaris ENSCAFG000000054022 retrocopies
retro_cfam_1411, retro_cfam_1569,
Choloepus hoffmanni ENSCHOG000000053288 retrocopies
retro_chof_1301, retro_chof_1369, retro_chof_1492, retro_chof_199, retro_chof_2477, retro_chof_2506, retro_chof_452, retro_chof_571,
Callithrix jacchus ENSCJAG000000154244 retrocopies
retro_cjac_2355, retro_cjac_2593, retro_cjac_388, retro_cjac_3963,
Cavia porcellus ENSCPOG000000046651 retrocopy
retro_cpor_995,
Dipodomys ordii ENSDORG000000029742 retrocopies
retro_dord_608, retro_dord_758,
Equus caballus ENSECAG00000013915 2 retrocopies
retro_ecab_588, retro_ecab_96 ,
Echinops telfairi ENSETEG000000155003 retrocopies
retro_etel_1225, retro_etel_1757, retro_etel_857,
Felis catus ENSFCAG000000119423 retrocopies
retro_fcat_1462, retro_fcat_1490, retro_fcat_981,
Homo sapiens ENSG000001492734 retrocopies
retro_hsap_1124, retro_hsap_1655, retro_hsap_2736, retro_hsap_3552,
Gorilla gorilla ENSGGOG000000065194 retrocopies
retro_ggor_1248, retro_ggor_1509, retro_ggor_216, retro_ggor_878,
Loxodonta africana ENSLAFG000000042973 retrocopies
retro_lafr_278, retro_lafr_600, retro_lafr_861,
Macropus eugenii ENSMEUG000000115814 retrocopies
retro_meug_1724, retro_meug_399, retro_meug_431, retro_meug_774,
Myotis lucifugus ENSMLUG000000040793 retrocopies
retro_mluc_1092, retro_mluc_680, retro_mluc_934,
Macaca mulatta ENSMMUG000000090196 retrocopies
retro_mmul_1166, retro_mmul_1634, retro_mmul_1779, retro_mmul_1816, retro_mmul_665, retro_mmul_871,
Monodelphis domestica ENSMODG000000069451 retrocopy
retro_mdom_304,
Mustela putorius furoENSMPUG000000091973 retrocopies
retro_mputfur_412, retro_mputfur_443, retro_mputfur_936,
Mus musculus ENSMUSG000000307442 retrocopies
retro_mmus_1453, retro_mmus_1776,
Nomascus leucogenys ENSNLEG000000269152 retrocopies
retro_nleu_103, retro_nleu_236,
Oryctolagus cuniculus ENSOCUG000000224123 retrocopies
retro_ocun_11, retro_ocun_1934, retro_ocun_787,
Otolemur garnettii ENSOGAG000000053187 retrocopies
retro_ogar_1180, retro_ogar_1354, retro_ogar_1559, retro_ogar_1574, retro_ogar_2577, retro_ogar_2786, retro_ogar_999,
Pongo abelii ENSPPYG000000036884 retrocopies
retro_pabe_1367, retro_pabe_2274, retro_pabe_2933, retro_pabe_929,
Pteropus vampyrus ENSPVAG000000112711 retrocopy
retro_pvam_1388,
Rattus norvegicus ENSRNOG000000174183 retrocopies
retro_rnor_2328, retro_rnor_283, retro_rnor_930,
Sarcophilus harrisii ENSSHAG000000111981 retrocopy
retro_shar_705,
Sus scrofa ENSSSCG000000148554 retrocopies
retro_sscr_283, retro_sscr_556, retro_sscr_568, retro_sscr_900,
Tupaia belangeri ENSTBEG000000070534 retrocopies
retro_tbel_1194, retro_tbel_2090, retro_tbel_265, retro_tbel_4262,
Tursiops truncatus ENSTTRG000000058585 retrocopies
retro_ttru_1108, retro_ttru_1413, retro_ttru_1927, retro_ttru_50, retro_ttru_544,
Vicugna pacos ENSVPAG000000116152 retrocopies
retro_vpac_131, retro_vpac_145,


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