RetrogeneDB ID:

retro_ggal_4

Retrocopy
location
Organism:Chicken (Gallus gallus)
Coordinates:21:1261035..1262148(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGALG00000001078
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:gga-mir-3533
Ensembl ID:ENSGALG00000009621
Aliases:ACTB, Bact, actin
Description:gga-mir-3533 [Source:miRBase;Acc:MI0015386]


Retrocopy-Parental alignment summary:






>retro_ggal_4
GATGTCCCAGCTGTAATCTTTGACAACGGGTCTGGATTGTGCAAGGCGGGGATCGCAGGGGACGGTGGCCCAAGGTCAGT
TATCACATCGATCGTCGGTCGCTCAAGAGTCAAATCTGCAATGCTGGGAGCTGGGATGAAAGAGTACTACGTAGGAGAAG
AAGCTCAGTCCAAAAGAGGGATCCTGACTTTGAATTATCCCATTGACCATGGCATCGTTACATCCTGGGATGACATGGAA
AGGATCTGGAGACACGTCTATGACTACGAGCTGAGAGTGAAAGCCAGCGAAAGACCCGTGCTGCTCACAGAACCCCCCCT
CAACCCCCTGCAGAACCGGGAAAGAATGACTGAGATCATGTTTGAGGGCTTCATGGTGCCCGCCATGTACGTGGCAGTCC
AGGCTGCGTTGGCCCTCTACGCGTCTGCCCGCACCACCGGCATAGTTCTGGACAGCGGGGATGGCGTCACCCACACCGTC
CCCATTTACGAGGGGTACTGCCTGCCCCATGCCGTGTCCAGGCTGGATATCGCTGGCCGGGATATCACTGAGTATTTTAT
GAGGCTCCTTTTGGAGAGCGGATACTCTTTCGTTAGCACCGCTGAAAGGGAAATTGTGAAAGATATCAAAGAGAAGCTGT
GCTATGTGGCTCTAGACCCCACTCTGGAAATGAAAGCAAGTCCAGAAGAAATCATGAAAGAATACAGATTACCTGACAGC
AACATCATTCAGATAGGCAGCCAGCTCTTTCGTGCACCAGAGACCCTTTTTGTACCTGCCAACGTTGGCATTGAAGCAGC
TGGTGTGCACAAAATGCTCTTCAACAGCGTCACAAAGTGCGACATCGATGTGCGCAGGGATCTGTATGGCAACGTGCTGC
TCTCGGGAGGCTCCACGCTCTTCCCTGGCCTGGAGGAGCGCATCCTGAAGGAGATGCACCTGCAGGTGCCTGTGGGGATG
CTCGTGAAAATCATTGCCCCTCCCGAGAGGAAGTACAGCGTGTGGGTCGGGGCCTCCGTCCTCTCCTGCCTGACCTCCTT
CAAATCAATGTGGATCACCGTGAGGGACTACGGGGATTTTGGGGCAGCTGTCGTCCACCGGAAATGCTGTTAA

ORF - retro_ggal_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.26 %
Parental protein coverage: 98.93 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEH
D..A...DNGSG.CKAG.AGD..PR.V..SIVGR.R....M.G.G.K..YVG.EAQSKRGILTL.YPI.H
RetrocopyDVPAVIFDNGSGLCKAGIAGDGGPRSVITSIVGRSRVKSAMLGAGMKEYYVGEEAQSKRGILTLNYPIDH
ParentalGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLY
GIVT.WDDME.IW.H....ELRV...E.PVLLTE.PLNP..NRE.MT.IMFE.F..PAMYVA.QA.L.LY
RetrocopyGIVTSWDDMERIWRHVYDYELRVKASERPVLLTEPPLNPLQNRERMTEIMFEGFMVPAMYVAVQAALALY
ParentalASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIK
AS.RTTGIV.DSGDGVTHTVPIYEGY.LPHA..RLD.AGRD.T.Y.M..L.E.GYSF..TAEREIV.DIK
RetrocopyASARTTGIVLDSGDGVTHTVPIYEGYCLPHAVSRLDIAGRDITEYFMRLLLESGYSFVSTAEREIVKDIK
ParentalEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIM
EKLCYVALD...EM...AS.....K.Y.LPD...I.IG...FR.PE.LF.P...G.E..G.H...FNS..
RetrocopyEKLCYVALDPTLEM--KASPEEIMKEYRLPDSNIIQIGSQLFRAPETLFVPANVGIEAAGVHKMLFNSVT
ParentalKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQ
KCD.D.R.DLY.N..LSGG.T..PG...R..KE.....P..M..KIIAPPERKYSVW.G.S.L..L..F.
RetrocopyKCDIDVRRDLYGNVLLSGGSTLFPGLEERILKEMHLQVPVGMLVKIIAPPERKYSVWVGASVLSCLTSFK
ParentalQMWISKQEYDESGPSIVHRKC
.MWI....Y...G...VHRKC
RetrocopySMWITVRDYGDFGAAVVHRKC

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 1212 .09 RPM
SRP007412_cerebellum 0 .00 RPM 1107 .92 RPM
SRP007412_heart 0 .05 RPM 600 .17 RPM
SRP007412_kidney 0 .00 RPM 1468 .61 RPM
SRP007412_liver 0 .00 RPM 2239 .38 RPM
SRP007412_testis 182 .92 RPM 603 .54 RPM

ChIP-Seq - click to see more details

Gallus gallus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ggal_4 retrocopy.

TSS - click to see more details

Gallus gallus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggal_4 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggal_4 has 1 orthologous retrocopies within neognath group .

Species RetrogeneDB ID
Meleagris gallopavo retro_mgal_6
Parental genes homology:
Parental genes homology involve 21 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus ENSGALG00000009621 1 retrocopy
retro_ggal_4 ,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus ENSRNOG0000003425410 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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