RetrogeneDB ID:

retro_psin_35

Retrocopy
location
Organism:Chinese softshell turtle (Pelodiscus sinensis)
Coordinates:JH206637.1:6056019..6056459(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPSIG00000009200
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS11
Ensembl ID:ENSPSIG00000011089
Aliases:None
Description:ribosomal protein S11 [Source:HGNC Symbol;Acc:10384]


Retrocopy-Parental alignment summary:






>retro_psin_35
CAACAGCCTACCATCTTCCAGAACAAGAAGTGGGTGCTTCTGGAAGAGGGAGGCAAGGAGAAACTCCCCCGTTACTACAA
GAACATTGGCTTGAACTTCAAAATCCCCAATGAGGCCATTGAGGGAACTTATATTGACAAGAAATGCCCTTTCACTGGCA
ATGTTTCTATCCGAGGTCTTATCCTGTCAGGTGTGGTTATCAAGAAGAAGATGCAGAGTACTATTATCATCCGCAGGGAT
TACTTACATTATATCTGCAAGTACAACCATTTTGAGAAATGCCACAAGAACATGTCTATGCACCTCTCCCCTGCTTCAGG
GATGTCCAGATTGGTGATACTGTGATTGTGGGGGAATGCCGTCCCCTCAGCAAGACAATCTGATTCAACGTCCTCAAGGT
CACAAAGGCTGCTGGCACCAAGAACCAGTTCCAGAAGTTT

ORF - retro_psin_35 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.81 %
Parental protein coverage: 70.67 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKQPTIFQNKKRVLLGEGGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVTKMK
.QPTIFQNKK.VLL.EGGKEKLPRYYKNIGL.FK.P.EAIEGTYIDKKCPFTGNVSIRG.ILSGVV.K.K
RetrocopyQQPTIFQNKKWVLLEEGGKEKLPRYYKNIGLNFKIPNEAIEGTYIDKKCPFTGNVSIRGLILSGVVIKKK
ParentalMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLS-PCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAG
MQ.TI.IRRDYLHYI.KYN.FEK.HKNMS.HLS.PCFRDVQIGD.V.VGECRPLSKT..FNVLKVTKAAG
RetrocopyMQSTIIIRRDYLHYICKYNHFEKCHKNMSMHLS<PCFRDVQIGDTVIVGECRPLSKTI*FNVLKVTKAAG
ParentalTKKQFQKF
TK.QFQKF
RetrocopyTKNQFQKF

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






RNA-Seq - click to see more details

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_psin_35 retrocopy.

TSS - click to see more details

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_psin_35 was not experimentally validated.

Retrocopy orthology:
Pelodiscus sinensis 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 17 parental genes, and 100 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001402013 retrocopies
retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus ENSBTAG000000139245 retrocopies
retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris ENSCAFG000000036319 retrocopies
retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus ENSCJAG000000000691 retrocopy
retro_cjac_340,
Danio rerio ENSDARG000000530581 retrocopy
retro_drer_15,
Equus caballus ENSECAG000000003701 retrocopy
retro_ecab_868,
Felis catus ENSFCAG0000000919613 retrocopies
retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Macropus eugenii ENSMEUG000000086492 retrocopies
retro_meug_1176, retro_meug_1640,
Monodelphis domestica ENSMODG000000134347 retrocopies
retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Otolemur garnettii ENSOGAG000000046277 retrocopies
retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Pelodiscus sinensis ENSPSIG00000011089 1 retrocopy
retro_psin_35 ,
Pan troglodytes ENSPTRG000000112991 retrocopy
retro_ptro_88,
Rattus norvegicus ENSRNOG0000002059518 retrocopies
retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus ENSSARG000000032362 retrocopies
retro_sara_11, retro_sara_469,
Sarcophilus harrisii ENSSHAG000000049911 retrocopy
retro_shar_649,
Ictidomys tridecemlineatus ENSSTOG000000234432 retrocopies
retro_itri_1033, retro_itri_805,
Tupaia belangeri ENSTBEG0000001667716 retrocopies
retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,


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