RetrogeneDB ID:

retro_btau_96

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:12:18173184..18173958(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000003560
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL8
Ensembl ID:ENSBTAG00000026327
Aliases:None
Description:60S ribosomal protein L8 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0S6]


Retrocopy-Parental alignment summary:






>retro_btau_96
ATGGGCCGTGTGATCCATGGGCAGAGGAAGGGCGCCAGCTCCGTGTTCCGCGCACATGTGAAGCACAGAAAAGGCGCTGC
GCGCCTACGCGCCGTGGATTTCGCCGAGCGACACGGATATATCAAGGGCATCGTGAAGGACGTCATCCACGACCCGGGCC
GCGGAGCACCCCTTGCCAAAGTGGTTTTCCGGGATCCGTACCGTTTTAAGAAGCGGACAGAGCTGTTCATCGCTGCTGAG
GGCATCCACACCGGCCAGTCTGGGTACTGTGGCAAGAAGGCCCAGCTCAACATCGGCAACGTGCTCCCGGTGGGCACCAT
GCCTGAGGGCACCATCGTGTGTTGTCTGGAGGAGAAGCCTGGTGACCGAGGCAAGCTGGCAAGAGCCTCCGGAAACTATG
CCACAGTCATCTCCCACAGCCCTGAGACAAAGAAGACGCGAGTGAAGCTGCCTTCGGGCTCCAAAAAGGTCATCTCCTCT
GCCAACAGAGCTGTGGTCGGTGTGGTGGCTGGAGGTGGCTGCATTGACAAGCCCATTCTGAAGGCTGGCCATGCCTACCA
CAAGTATAAGGCAAAGAGGAACTGCTGGCCACTGGTGCGGGGTGTGGCCATGAACCCTGTCGAGCATCCCTTCGGAGGTG
GCAACCACCAGCACATCGGCAAACCCTCTACTATCCGCAGAGATGCCCCTGCTGGCCGGAAAGTGGGTCTCATTGCTGCC
CTCCGGACTGGCCGTCTCCGGGGAACCAAGACTGTGCAGGAGAAGGAGAACTAG

ORF - retro_btau_96 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
MGRVI.GQRKGA.SVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKD.IHDPGRGAPLAKVVFRDPYRFK
RetrocopyMGRVIHGQRKGASSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDVIHDPGRGAPLAKVVFRDPYRFK
ParentalKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
KRTELFIAAEGIHTGQ..YCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISH.
RetrocopyKRTELFIAAEGIHTGQSGYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHS
ParentalPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
PETKKTRVKLPSGSKKVISSANRAVVGVVAGGG.IDKPILKAG.AYHKYKAKRNCWP.VRGVAMNPVEHP
RetrocopyPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGCIDKPILKAGHAYHKYKAKRNCWPLVRGVAMNPVEHP
ParentalFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
FGGGNHQHIGKPSTIRRDAPAGRKVGLIAA.RTGRLRGTKTVQEKEN
RetrocopyFGGGNHQHIGKPSTIRRDAPAGRKVGLIAALRTGRLRGTKTVQEKEN

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
ERP005899_liver 0 .07 RPM 44 .27 RPM
ERP005899_muscle 1 .85 RPM 1288 .85 RPM
SRP017611_brain 0 .23 RPM 91 .72 RPM
SRP017611_kidney 0 .47 RPM 211 .36 RPM
SRP017611_liver 0 .15 RPM 139 .09 RPM
SRP030211_testis 0 .32 RPM 117 .74 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_96 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_96 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_96 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000179331 retrocopy
retro_acar_31,
Ailuropoda melanoleuca ENSAMEG000000053951 retrocopy
retro_amel_241,
Bos taurus ENSBTAG00000026327 1 retrocopy
retro_btau_96 ,
Canis familiaris ENSCAFG000000016771 retrocopy
retro_cfam_1132,
Callithrix jacchus ENSCJAG000000213884 retrocopies
retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus ENSCPOG000000038542 retrocopies
retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus ENSDNOG000000093002 retrocopies
retro_dnov_2505, retro_dnov_503,
Echinops telfairi ENSETEG000000071044 retrocopies
retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus ENSFCAG000000262881 retrocopy
retro_fcat_570,
Homo sapiens ENSG000001610161 retrocopy
retro_hsap_2851,
Gorilla gorilla ENSGGOG000000081641 retrocopy
retro_ggor_1974,
Macropus eugenii ENSMEUG000000138249 retrocopies
retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta ENSMMUG000000133792 retrocopies
retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica ENSMODG000000042833 retrocopies
retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furoENSMPUG000000060221 retrocopy
retro_mputfur_1517,
Mus musculus ENSMUSG000000039702 retrocopies
retro_mmus_2004, retro_mmus_2112,
Nomascus leucogenys ENSNLEG000000109522 retrocopies
retro_nleu_1603, retro_nleu_594,
Ornithorhynchus anatinus ENSOANG000000026461 retrocopy
retro_oana_93,
Oryctolagus cuniculus ENSOCUG000000247161 retrocopy
retro_ocun_146,
Pan troglodytes ENSPTRG000000207161 retrocopy
retro_ptro_1931,
Rattus norvegicus ENSRNOG000000485232 retrocopies
retro_rnor_122, retro_rnor_239,
Sarcophilus harrisii ENSSHAG000000135682 retrocopies
retro_shar_482, retro_shar_558,
Tupaia belangeri ENSTBEG000000103632 retrocopies
retro_tbel_2826, retro_tbel_3453,
Tursiops truncatus ENSTTRG000000138581 retrocopy
retro_ttru_1147,


Copyright © RetrogeneDB 2014-2017