RetrogeneDB ID:

retro_amel_465

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192458.1:211497..212207(+)
Located in intron of:ENSAMEG00000009637
Retrocopy
information
Ensembl ID:ENSAMEG00000009722
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3
Ensembl ID:ENSAMEG00000017051
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_465
GCGCGCAGCGGCAAGATGGCGGCGCACATTTCCAAGAAGAGGAAGTTTGTAGCCGATGGCGTCTTCAAAGCCCAGCTGAA
CGGGTTTCCCACTCAGGAGCTGGCTGAAGGTGGCTACTCCAGAGTGGAGGTCCGCGTTACACCAACCAGGACAGAAATCA
TTGTCTTGGGCACCAGGACACAGAAGGCTCTTGGTGAGAAGGGCCAGCGGATCCGGGGATTGACTGCTGTGGTTCGGAAG
GGCTTTGGTTTCCCTGAGGGCGTGGAGAGCTCTGTGCTGAAAAGGTGGCCACGAGAGGTCTGCGGGCTGTCACCAGGCCC
AGTCTCTGCATCACAGGCTCCTTCCTAGGAGGCCTTGCTGTGCAGAGGGCCTGCTCTGCTGTGCCACGGTGCATTATGGA
GAGCGGGGCTAAAGACTGTGAGGTCCTGGTGTCTGGGAAACTCCAAGGCCAAAGGGCTAAATCCATGAAGGGTGTGGATG
GCCTGATGATTCGCAGTGAGGACTTTGTGAACTACTGCATTGACACTGCTGTGGGCCATGTGCCACTCAGACAGGGTGCG
CTGGGCATCAAAGCGAAGATCGTGCTTCCCTGGGGCCCGAGTGCTAAGATTGGCCCTAAGAAGCCCCTGCCTGACCACGT
GAGCATTGTGGAACCCAAAGATGAGATACTGCCCATCACTCCCATGTTGGAACAGTAGGGTGAGAAGCCA

ORF - retro_amel_465 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.37 %
Parental protein coverage: 95.16 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalARGGKMAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRR
AR.GKMA..ISKKRKFVADG.FKA.LN.F.T.ELAE.GYS.VEVRVTPTRTEII.L.TRTQ..LGEKG.R
RetrocopyARSGKMAAHISKKRKFVADGVFKAQLNGFPTQELAEGGYSRVEVRVTPTRTEIIVLGTRTQKALGEKGQR
ParentalIRELTAVVQKRFGFPEGSV-ELYAEKVATRGLCAIAQAE-SLRYKLLGGLAVRRACYGVLRFIMESGAKG
IR.LTAVV.K.FGFPEG...EL.AEKVATRGL.A............LGGLAV.RAC..V.R.IMESGAK.
RetrocopyIRGLTAVVRKGFGFPEGVE<ELCAEKVATRGLRAVTRPSLCITGSFLGGLAVQRACSAVPRCIMESGAKD
ParentalCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKKP
CEV.VSGKL.GQRAKSMK.VDGLMI.S.D.VNY..DTAV.HV.LRQG.LGIK.KI.LPW.PS.KIGPKKP
RetrocopyCEVLVSGKLQGQRAKSMKGVDGLMIRSEDFVNYCIDTAVGHVPLRQGALGIKAKIVLPWGPSAKIGPKKP
ParentalLPDHVSIVEPKDEILPTTPISEQKGGKP
LPDHVSIVEPKDEILP.TP..EQ.G.KP
RetrocopyLPDHVSIVEPKDEILPITPMLEQ*GEKP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_465 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_465 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 30 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000017051 2 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 ENSECAG000000139152 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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