RetrogeneDB ID:

retro_meug_1230

Retrocopy
location
Organism:Wallaby (Macropus eugenii)
Coordinates:Scaffold334079:761..1777(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSMEUG00000016247
Aliases:None
Description:actin, gamma 1 [Source:HGNC Symbol;Acc:144]


Retrocopy-Parental alignment summary:






>retro_meug_1230
CCTAGACATCAGAGTGTGATGATGAGTATGGGCCAGAAAGACAGCTAGATGGGGGATAAGGCCCAGAAGGGGAGAGGTAT
TCTGACCCTGAAGTACCCCAATGAACATGGTACTGTCACCAATTGGGATGACATGGAGAAGATTTGGCATCATACTTTCT
ACAGTGAGCTCCGTGTGGCCCCTGAAGAGTACCCTGTGCTGCTCACAGAAGCCCCCCTGAACCCCAAAACCAACAGAGAA
AAGATGACTCAGATTATGTTTGAGACCTTCAACACCCTGGTCATGTATGTTGCCATCCAGGCTGTGCTGTCCCTGTATGC
CTCTGGTCATACCACTGGTATTGTGATGGACTCCGGTGATGGTGTGACCCACACTGTGCCCATCTATGAAGGTTATGCCC
TTCCCCATGCCATCCTCCATCTGGATCTGGCTGGCTATGCTCTGATGGATTACCTCATGAAGACCCTGACGGAGATAGGG
TACAAGTTTCACTACCACAGCTGAGAGGGAAATCATGTGTGACATCAAGGAGAAGCTGTGTTACATCACCCTAGACTTTG
AGCAGGAGATGGCCACTGATGCATCTAGCTTCTCTCTGGAAAAAAGAGCTATGAGCTCCCTGATGGTCAAGTTATCACCA
ATGGCAATCAGAGATTCCCGGTGCCCAGAAGCTCTCTTCCAGCCATCTTTCTTAGGTATGGAATTCTGTGGAAACCACGA
AACTACCTTCAACTCAATTATGAAGTGTGGTGTTGACATCCTTAAGGATTTGTATGCCAATACTGTACTGTCTGGTGGTA
CCACTATGTGCCCAGGCATTGCTGACAGGATGCAGAAGGAGATAACAGCCCTAGCTCCCAGCACAATGAAAATCAAGATC
ATTGCCCCACCTCAGCGCAAATACTGTCTGGATTGGAGGCTCCATCCTGGCATCTCTTTCCACCTTCCAGCAGATGTGGA
TCAACAAGCAGGAGTATGATGAATCTGGGCCCTCCACTGTCCACCACAAATGCTTC

ORF - retro_meug_1230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.55 %
Parental protein coverage: 90.13 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTE
PRHQ.VM..MGQKDS..GD.AQ..RGILTLKYP.EHG.VTNWDDMEKIWHHTFY.ELRVAPEE.PVLLTE
RetrocopyPRHQSVMMSMGQKDS*MGDKAQKGRGILTLKYPNEHGTVTNWDDMEKIWHHTFYSELRVAPEEYPVLLTE
ParentalAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILR
APLNPK.NREKMTQIMFETFNT..MYVAIQAVLSLYASG.TTGIVMDSGDGVTHTVPIYEGYALPHAIL.
RetrocopyAPLNPKTNREKMTQIMFETFNTLVMYVAIQAVLSLYASGHTTGIVMDSGDGVTHTVPIYEGYALPHAILH
ParentalLDLAGRDLTDYLMKILTERGY-SFTTTAEREIVRDIKEKLCYVALDFEQEMAT-AASSS-SLEKSYELPD
LDLAG..L.DYLMK.LTE.GY.SFTTTAEREI..DIKEKLCY..LDFEQEMAT.A.S.S.S..KSYELPD
RetrocopyLDLAGYALMDYLMKTLTEIGY>SFTTTAEREIMCDIKEKLCYITLDFEQEMATDASSFS<SGKKSYELPD
ParentalGQVITIGNERF-RCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRM
GQVIT.GN.RF.RCPEALFQPSFLGME.CG.HETTFNSIMKC.VDI.KDLYANTVLSGGTTM.PGIADRM
RetrocopyGQVITNGNQRF>RCPEALFQPSFLGMEFCGNHETTFNSIMKCGVDILKDLYANTVLSGGTTMCPGIADRM
ParentalQKEITALAPSTMKIKIIAPPERKY-SVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF
QKEITALAPSTMKIK.I..P......VWIGGSILASLSTFQQMWI.KQEYDESGPS.VH.KCF
RetrocopyQKEITALAPSTMKIK-IIAPPQRK>TVWIGGSILASLSTFQQMWINKQEYDESGPSTVHHKCF

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






RNA-Seq - click to see more details

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Macropus eugenii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_meug_1230 retrocopy.

TSS - click to see more details

Macropus eugenii was not studied using FANTOM5 data.

Lab - click to see more details

retro_meug_1230 was not experimentally validated.

Retrocopy orthology:
Macropus eugenii 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 20 parental genes, and 103 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Bos taurus ENSBTAG000000061892 retrocopies
retro_btau_286, retro_btau_903,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Macropus eugenii ENSMEUG000000054631 retrocopy
retro_meug_970,
Macropus eugenii ENSMEUG000000108431 retrocopy
retro_meug_1374,
Macropus eugenii ENSMEUG00000016247 57 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,
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,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Otolemur garnettii ENSOGAG000000080403 retrocopies
retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sorex araneus ENSSARG000000121971 retrocopy
retro_sara_267,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Tupaia belangeri ENSTBEG000000107811 retrocopy
retro_tbel_422,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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