RetrogeneDB ID:

retro_amel_1553

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193606.1:485049..485477(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PIN4
Ensembl ID:ENSAMEG00000005801
Aliases:None
Description:protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin) [Source:HGNC Symbol;Acc:8992]


Retrocopy-Parental alignment summary:






>retro_amel_1553
ACACTGGAGTTGAGAGTTCAGCTGCAAGTTTCACAGATGCTGCCCAAGGGAAAAAGCAATTCCAGGGAAGGGAAGAGAGG
GGGAGCAGCCTCCAGGAGTGACAGTTCTGACAAGAAGACTCACGGTCCCACAGGTGGTGGCAATGGAGTAAAGGTCAGAC
ACATTCAGTGAGAAAAACATGGAAAAATTATGGAAGCCATGGAAAAGTTAAAGTCTGGAATGAGATTCAATGAAGTGGCT
GCACAGTGTAGTGAAGATAAAGCCAGCCAAGGGGACACTTGGGTTGGATGACCAGAGATTCCATGGTGGGACCATTTCAA
GAAGAAGCATTTGCCTTGCTTGTGAGTGGGCTGGCTAAACCTGTGTTTACGGACCCTCCGGTTAAGATAAAATTTGGATA
TCATATTATTATGGTTAAAGGGAGAAAA

ORF - retro_amel_1553 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.39 %
Parental protein coverage: 94.7 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTKPLRFLPQVPRMPPKGKSGSGKGGKGGAASGSDSSDKKAQGPKGGGSAVKVRHILCEKHGKIMEAMEKL
T..LR...QV..M.PKGKS.S..G..GGAAS.SDSSDKK..GP.GGG..VKVRHI..EKHGKIMEAMEKL
RetrocopyTLELRVQLQVSQMLPKGKSNSREGKRGGAASRSDSSDKKTHGPTGGGNGVKVRHIQ*EKHGKIMEAMEKL
ParentalKSGMRFSEVATQYSEDKARQG-GDLGWMTRGSMVGPFQEAAFALPVSGLDKPVFTDPPVKTKFGYHIIMV
KSGMRF.EVA.Q.SEDKA.QG.G.LGWMTR.SMVGPFQE.AFAL.VSGL.KPVFTDPPVK.KFGYHIIMV
RetrocopyKSGMRFNEVAAQCSEDKASQG<GHLGWMTRDSMVGPFQEEAFALLVSGLAKPVFTDPPVKIKFGYHIIMV
ParentalEGKK
.G.K
RetrocopyKGRK

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_1553 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1553 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 19 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000005801 1 retrocopy
retro_amel_1553 ,
Canis familiaris ENSCAFG000000322301 retrocopy
retro_cfam_212,
Callithrix jacchus ENSCJAG0000000499210 retrocopies
retro_cjac_1218, retro_cjac_1587, retro_cjac_1631, retro_cjac_1720, retro_cjac_1729, retro_cjac_1746, retro_cjac_1863, retro_cjac_2670, retro_cjac_2704, retro_cjac_2829,
Cavia porcellus ENSCPOG000000114011 retrocopy
retro_cpor_631,
Dipodomys ordii ENSDORG000000069852 retrocopies
retro_dord_109, retro_dord_352,
Felis catus ENSFCAG000000120365 retrocopies
retro_fcat_1325, retro_fcat_1411, retro_fcat_581, retro_fcat_723, retro_fcat_769,
Homo sapiens ENSG000001023093 retrocopies
retro_hsap_1562, retro_hsap_1604, retro_hsap_304,
Gorilla gorilla ENSGGOG000000160084 retrocopies
retro_ggor_1187, retro_ggor_1210, retro_ggor_328, retro_ggor_338,
Loxodonta africana ENSLAFG000000182611 retrocopy
retro_lafr_212,
Macropus eugenii ENSMEUG000000036111 retrocopy
retro_meug_368,
Microcebus murinus ENSMICG000000016404 retrocopies
retro_mmur_138, retro_mmur_294, retro_mmur_483, retro_mmur_674,
Myotis lucifugus ENSMLUG000000120732 retrocopies
retro_mluc_2189, retro_mluc_923,
Mustela putorius furoENSMPUG000000052873 retrocopies
retro_mputfur_1285, retro_mputfur_417, retro_mputfur_858,
Mus musculus ENSMUSG000000794808 retrocopies
retro_mmus_1656, retro_mmus_1703, retro_mmus_2205, retro_mmus_2741, retro_mmus_2921, retro_mmus_3673, retro_mmus_399, retro_mmus_821,
Nomascus leucogenys ENSNLEG000000181191 retrocopy
retro_nleu_2957,
Oryctolagus cuniculus ENSOCUG000000087152 retrocopies
retro_ocun_137, retro_ocun_835,
Pongo abelii ENSPPYG000000204602 retrocopies
retro_pabe_146, retro_pabe_384,
Rattus norvegicus ENSRNOG000000500516 retrocopies
retro_rnor_1755, retro_rnor_2368, retro_rnor_2575, retro_rnor_2576, retro_rnor_480, retro_rnor_553,
Sorex araneus ENSSARG000000037322 retrocopies
retro_sara_201, retro_sara_248,


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