RetrogeneDB ID:

retro_psin_42

Retrocopy
location
Organism:Chinese softshell turtle (Pelodiscus sinensis)
Coordinates:JH207674.1:296913..297519(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ST13
Ensembl ID:ENSPSIG00000004553
Aliases:None
Description:suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) [Source:HGNC Symbol;Acc:11343]


Retrocopy-Parental alignment summary:






>retro_psin_42
GAAAAGAAAACCAAGGAGGAAGGGTCACCAGAGGCAGCAGAGATCAAGGAGAGTGATTTGGAAATTGATGGTGATGTTGA
ACCAGATCTGGATGGTTCCCAAGAAATAGGAGATGAACATTTGGTAGTAACAAATGAATTGATAGACTCTGCCAACAGAA
AAAGGAAAGAGGCCTTTTCCTCTCTAGAGAAAGGTGACCTTCAGAAAGCTATGGATTTGTTCACAGATGCTATCAAGCTG
AATCCTCACTTCCACCTCTCATATGTTAATCGAGCCAGTGTCTTTTTGAAACTACAGAAGCCAAATGCTGCCATTAGAGA
CTGTGACAGAGCCTGTGAGCTTAACCCCAATTCAGCACAGTCTTACAAGTGGAGAGGGCAAGCACACATGCTCCTGGGAT
GCTGGGAAAAGGCAGCTCAGGACTTGACCTTGGCATGTCAACTGGATTATGATGAAAACACTTATACCAGGCTAAAAAAG
GTGCTAATGGCTGAGAAGATTGCTGCACATCAGGCAGAGTATGAGCAAAAATGTGCATTAAGGGAGATACAGGAAAGGCT
GGAAAGGGTGAAACTGGCCTTGGAGGAGGAAGAAAGAATCCAGAGG

ORF - retro_psin_42 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.54 %
Parental protein coverage: 63.08 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalEKQPEEPVKSPEPESEESDLEIDNEGVIEPDKDDPQEMGDENVEVTEEMMDQADEKKIEGIHALGEGELQ
EK...E.......E..ESDLEID..G..EPD.D..QE.GDE...VT.E..D.A..K..E....L..G.LQ
RetrocopyEKKTKEEGSPEAAEIKESDLEID--GDVEPDLDGSQEIGDEHLVVTNELIDSANRKRKEAFSSLEKGDLQ
ParentalKAIDLFTEAIKLNPHLAILYAKRASVFVKLQKPNAAIRDCDRAIQINPDSAQTYKWRGKAHRLLGHWEEA
KA.DLFT.AIKLNPH....Y..RASVF.KLQKPNAAIRDCDRA...NP.SAQ.YKWRG.AH.LLG.WE.A
RetrocopyKAMDLFTDAIKLNPHFHLSYVNRASVFLKLQKPNAAIRDCDRACELNPNSAQSYKWRGQAHMLLGCWEKA
ParentalVHDLALACKLDYDEEASAMLKEVQPRAQKIVEHRRKYERKREEKEIKERLERVKKAREEHERAQR
..DL.LAC.LDYDE.....LK.V...A.KI..H...YE.K....EI.ERLERVK.A.EE.ER.QR
RetrocopyAQDLTLACQLDYDENTYTRLKKVL-MAEKIAAHQAEYEQKCALREIQERLERVKLALEEEERIQR

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_42 retrocopy.

TSS - click to see more details

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_psin_42 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 16 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000052271 retrocopy
retro_acar_2,
Ailuropoda melanoleuca ENSAMEG000000138801 retrocopy
retro_amel_135,
Bos taurus ENSBTAG000000062024 retrocopies
retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris ENSCAFG0000000113914 retrocopies
retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Callithrix jacchus ENSCJAG0000000464411 retrocopies
retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus ENSCPOG000000022904 retrocopies
retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus ENSFCAG000000118472 retrocopies
retro_fcat_920, retro_fcat_987,
Gorilla gorilla ENSGGOG0000002674716 retrocopies
retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Myotis lucifugus ENSMLUG000000077642 retrocopies
retro_mluc_1088, retro_mluc_2021,
Macaca mulatta ENSMMUG000000191183 retrocopies
retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica ENSMODG000000130422 retrocopies
retro_mdom_1087, retro_mdom_31,
Otolemur garnettii ENSOGAG000000169321 retrocopy
retro_ogar_224,
Pongo abelii ENSPPYG0000001185814 retrocopies
retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pelodiscus sinensis ENSPSIG00000004553 1 retrocopy
retro_psin_42 ,
Sarcophilus harrisii ENSSHAG000000003192 retrocopies
retro_shar_70, retro_shar_767,
Ictidomys tridecemlineatus ENSSTOG000000031651 retrocopy
retro_itri_88,


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