RetrogeneDB ID:

retro_amel_194

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192350.1:1855315..1856128(-)
Located in intron of:ENSAMEG00000017771
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RNPS1
Ensembl ID:ENSAMEG00000017861
Aliases:None
Description:RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]


Retrocopy-Parental alignment summary:






>retro_amel_194
GCTCCTTCTCCTACCAAATGCAAAGATCACCCTGATGAGAAGTCCAAGGATCATGCTAAAGAGAAAGGGATCCCCAAGGA
GTGGAGCAAGGATGGTGACAGGGATAAAACTCAGAAGAAGTACAGTCCTTGCAAGTGTGGCAGCAGCACCAGGTCACAGT
GCAACTCTCCTTCCAGCACCAGCACAGGCTTGAGCAATGGCTCAAGCTCCTCTTCTGTGTCCAATTTCTGAGGAAGTTCA
GCATGTCCTACAGCTCCAATTCCAGCAGCTCCTCTAACTCAACCAGTACCTCTGGGTGTTGGCATGACAACAGGCAGCGT
TCCCGCTCCAAACCCGAACCACCCAAAAGAGATGAAAAGGAAAGGAAAAACTGGAGTCCTTCCCCCGGCCAAAGTGTACA
CCAGGAGGCTCACCAGGAATGTGAGCAAGGACCACATCACGGAGATACTCTCCACCTCTGAGAAAATTAACAGATTGACA
TGCTTGTAAAAAGCTGTCACCCATCTTTCTAAAGGCTATGCATACATGGAGTCAGAATACCCAGATGAAGCCAAGAAGGT
GGTAAAGGACATGGATGAAGGACAAATCGATGGCCAGGAGATCACTACCACCACTGTGCTGGCCTACGTTGCCCCCCCGC
CATGGGAATTCAGCCCTCCCAGGAGAATGCTGCCACCACCCCCCACGTGGCACTAGTCACCCCTGCAGATGAGATGATTG
AGTTCCCTGAGGGGCAGTCCCCTGTGCGCCAGGCAATGTCGCTCCCCTGGCTGCTGCTGCCACGGCAGCCACTCCAGCTC
CAATCCCTCCCAA

ORF - retro_amel_194 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.49 %
Parental protein coverage: 92.13 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGSS
APSPTK.KD..DEKSKD..K.KG..KE.S.KD..RDKT.K..S.....SSTR....S...S.SSTSTG.S
RetrocopyAPSPTKCKDHPDEKSKDHAKEKGIPKEWS-KDGDRDKTQKKYSPCKCGSSTR----SQCNSPSSTSTGLS
ParentalSGSSSSSASSRSGSS-STSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKP-TK
.GSSSSS.S...GSS.S.S.SS.SSSSS.S.S.S...HDNR.RSRSK..PPKRDEKER.....SP.P..K
RetrocopyNGSSSSSVSNF*GSS<SMSYSSNSSSSSNSTSTSGCWHDNRQRSRSKPEPPKRDEKER--KNWSPSP>AK
ParentalVHIGRLTRNVTKDHIMEIFSTYGKIK-MIDMPVE-RMHP-HLSKGYAYVEFENPDEAEKALKHMDGGQID
V...RLTRNV.KDHI.EI.ST..KI...IDM.V.....P.HLSKGYAY.E.E.PDEA.K..K.MD.GQID
RetrocopyVYTRRLTRNVSKDHITEILSTSEKIN<QIDMLVK<KLSP<HLSKGYAYMESEYPDEAKKVVKDMDEGQID
ParentalGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRS
GQEIT.T.VLA....PPP..FSPPRRMLPPPP.W..SP..MR..S.S.R......R..RSPG...H.S.S
RetrocopyGQEITTTTVLA-YVAPPPWEFSPPRRMLPPPPTWH*SPLQMR*LS-SLRGSPLCARQCRSPGCCCHGSHS
ParentalSSNSSR
SSN.S.
RetrocopySSNPSQ

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_194 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_194 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 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000017861 1 retrocopy
retro_amel_194 ,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Rattus norvegicus ENSRNOG000000087034 retrocopies
retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,




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