RetrogeneDB ID:

retro_psin_4

Retrocopy
location
Organism:Chinese softshell turtle (Pelodiscus sinensis)
Coordinates:JH209271.1:2026057..2027185(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPSIG00000001325
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSPSIG00000002102
Aliases:None
Description:actin, gamma 1 [Source:HGNC Symbol;Acc:144]


Retrocopy-Parental alignment summary:






>retro_psin_4
ATGTTTGACCCCAAACTTTTAGATATCCCAGCTGTGATCTTTGACAATGGGTCTGGACTGTGCAAAGCGGGTATTGCCGG
GGACAGCGCTCCCCGGTCGGTTATTACAGCTATTGTGGGCCGCTCGAAAGCCAAAGCGACAATGCTAGGAGCGGGCCAGA
AGGAATATTACGTGGGAGAAGAAGCCCAGTCCAAGAGGGGAGTCTTATCATTGAATTATCCAATCGACCATGGCATCGTT
ACCTCCTGGGATGACATGGAGAGGATCTGGAGGCACGTCTATGAGTGTGAGCTGAGAATCAAAGCCAGCGACAGGCCGGT
GCTACTGACAGAAGCCCCACTCAATCCCCTGCAGAACCGGGAAAAAATGACCGAGATCATGTTTGAAGGCTTTAAGGTGC
CTGCCATGTATGTTGCTGTCCAGGCGACGCTGGCTCTCTACGCATCCGCACGCACAACGGGGATAGTGATGGACAGTGGC
GATGGAGTTACCCACACGGTCCCCATCTATGAAGGATACTGTTTACCCCATGCTGTTTCCAGACTGGACATCGCAGGCAG
GGATATCACGGAATACTTCATGAGACTCCTTTTGGAAAGTGGGCACTCCTTTGTAAGCACAGCTGAGAGGGAGATTGTGA
AAGACATCAAGGAGAAGCTGTGCTACGTGGCTCTAGATCCCATCCAAGAAATGAAAGCAAAGCCGGAAGAAATCCTCAAA
GAATACAAACTGCCGGATGGAAATATCATTAAGATCGGCAACCAGCTCTTTCGAGCCCCGGAGACCCTTTTTATGCCAGC
CAACATTGGCATCGAAGCCCCCGGGGTGCACAAAATGATCTTCAACAGCGTCATGAAATGTGACATTGACGTTCGCAGGA
ATCTTTATGGCAACGTGCTGCTTTCCGGGGGGTCCACCCTCTTTCCGGGGCTGGATGAGCGGATCCTGAGGGAGATGCAG
CGGCAGGTGCCCATCGGGATGGCCGTACGCATCATAGCCCCGCCTGAGAGGAAGTACTGTGTGTGGATCGGCGCGTCCAT
CCTCACTTGCTTGTCATCTTTTAAACAGATGTGGGTCACCGTCAGCGATTACAAAGAGTTTGGGGCAGCCGTCGTGCACA
GGAAATGC

ORF - retro_psin_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.53 %
Parental protein coverage: 98.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEH
.I.A...DNGSG.CKAG.AGD.APR.V...IVGR......M.G.GQK..YVG.EAQSKRG.L.L.YPI.H
RetrocopyDIPAVIFDNGSGLCKAGIAGDSAPRSVITAIVGRSKAKATMLGAGQKEYYVGEEAQSKRGVLSLNYPIDH
ParentalGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLY
GIVT.WDDME.IW.H....ELR......PVLLTEAPLNP..NREKMT.IMFE.F..PAMYVA.QA.L.LY
RetrocopyGIVTSWDDMERIWRHVYECELRIKASDRPVLLTEAPLNPLQNREKMTEIMFEGFKVPAMYVAVQATLALY
ParentalASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIK
AS.RTTGIVMDSGDGVTHTVPIYEGY.LPHA..RLD.AGRD.T.Y.M..L.E.G.SF..TAEREIV.DIK
RetrocopyASARTTGIVMDSGDGVTHTVPIYEGYCLPHAVSRLDIAGRDITEYFMRLLLESGHSFVSTAEREIVKDIK
ParentalEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIM
EKLCYVALD..QEM...A......K.Y.LPDG..I.IGN..FR.PE.LF.P...G.E..G.H...FNS.M
RetrocopyEKLCYVALDPIQEM--KAKPEEILKEYKLPDGNIIKIGNQLFRAPETLFMPANIGIEAPGVHKMIFNSVM
ParentalKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQ
KCD.D.R..LY.N..LSGG.T..PG...R...E.....P..M...IIAPPERKY.VWIG.SIL..LS.F.
RetrocopyKCDIDVRRNLYGNVLLSGGSTLFPGLDERILREMQRQVPIGMAVRIIAPPERKYCVWIGASILTCLSSFK
ParentalQMWISKQEYDESGPSIVHRKC
QMW.....Y.E.G...VHRKC
RetrocopyQMWVTVSDYKEFGAAVVHRKC

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_4 retrocopy.

TSS - click to see more details

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab - click to see more details

retro_psin_4 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 26 parental genes, and 142 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Bos taurus ENSBTAG000000061892 retrocopies
retro_btau_286, retro_btau_903,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Macropus eugenii ENSMEUG0000001624757 retrocopies
retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus ENSMICG000000148633 retrocopies
retro_mmur_23, retro_mmur_352, retro_mmur_6,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG0000001338515 retrocopies
retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Otolemur garnettii ENSOGAG000000080403 retrocopies
retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis ENSPSIG00000002102 2 retrocopies
retro_psin_25, retro_psin_4 ,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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