RetrogeneDB ID:

retro_btau_376

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:10:51842780..51843483(-)
Located in intron of:ENSBTAG00000005479
Retrocopy
information
Ensembl ID:ENSBTAG00000011764
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CLNS1A
Ensembl ID:ENSBTAG00000019930
Aliases:None
Description:methylosome subunit pICln [Source:RefSeq peptide;Acc:NP_001069768]


Retrocopy-Parental alignment summary:






>retro_btau_376
AGCTTCCTCAGAAGTTTCCCGCCGCCTGGGTCGGCTGAGGGCCTACGGCAGCAGCAACCTGACACCAAGGCTGTGCTGAA
CGGGAAGGGCCTCCGGCACCCTTTACATCGCTGAAAGCCGCCTGTCTTGGTTAGATGGCTCTGGATTGGGATTCTCCCTG
GAACACCCCGCCATTAGTTTGCATGCAGTATCCAGGGACCTAAACGCCTATCCACGAGAGCATCTGTATGTTATGGTGAA
TGCCAAATTTGGAGAAGAATCAAAAGAATCGGTTGCTAATGAAGAAGAGGAAGATAGTGATGATGACATTGAACCAATTT
CTGAATTTAGATTTGTGCCTAGGCATAAATCAGCGTTGGAGGCAATGTTCATTGCAATGTGTGAATGCCAGGCTTTGCAT
CCAGATCCTGAGGATGAAGATTCAGATGATTACGATGGAGACGAATATGATGTGGAAGCCCATGAACAAGGGCAGGGGGA
CATCCCTACATTTTATACCTATGAAGAAGGATTATCCCATTTAACAGCAGAAGGCCAAGCCACACTGGAGAGATTGGAAG
GAATGCTTTCTCAGTCTGTGAGCAGCCAGTATAACATGGCTGGAGTCTGGACAGAAGATTCAATAAGAGATTATGAAGAT
GGGATGGAGGTAGATACTACACCAACAGTTGCTGGACAGTTTGAGGGTGCAGATGTTGATCAC

ORF - retro_btau_376 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.51 %
Parental protein coverage: 99.58 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSFLRSFPPPGSAEGLRQQQPDTEAVLNGKGL-GTGTLYIAESRLSWLDGSGLGFSLEYPTISLHAVSRDL
SFLRSFPPPGSAEGLRQQQPDT.AVLNGKGL.GT..LYIAESRLSWLDGSGLGFSLE.P.ISLHAVSRDL
RetrocopySFLRSFPPPGSAEGLRQQQPDTKAVLNGKGL>GT--LYIAESRLSWLDGSGLGFSLEHPAISLHAVSRDL
ParentalNAYPREHLYVMVNAKFGEESKESVADEEEEDSDDDIEPISEFRFVPSDKSALEAMFTAMCECQALHPDPE
NAYPREHLYVMVNAKFGEESKESVA.EEEEDSDDDIEPISEFRFVP..KSALEAMF.AMCECQALHPDPE
RetrocopyNAYPREHLYVMVNAKFGEESKESVANEEEEDSDDDIEPISEFRFVPRHKSALEAMFIAMCECQALHPDPE
ParentalDEDSDDYDGDEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDS
DEDSDDYDGDEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGV.TEDS
RetrocopyDEDSDDYDGDEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVWTEDS
ParentalVRDYEDGMEVDTTPTVAGQFEDADVDH
.RDYEDGMEVDTTPTVAGQFE.ADVDH
RetrocopyIRDYEDGMEVDTTPTVAGQFEGADVDH

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 17 .16 RPM
ERP005899_muscle 0 .00 RPM 23 .49 RPM
SRP017611_brain 0 .09 RPM 20 .74 RPM
SRP017611_kidney 0 .00 RPM 25 .13 RPM
SRP017611_liver 0 .00 RPM 9 .21 RPM
SRP030211_testis 0 .07 RPM 32 .49 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_376 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_376 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_376 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000019930 1 retrocopy
retro_btau_376 ,
Canis familiaris ENSCAFG000000049006 retrocopies
retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus ENSCJAG000000149271 retrocopy
retro_cjac_4085,
Cavia porcellus ENSCPOG000000052601 retrocopy
retro_cpor_67,
Felis catus ENSFCAG000000263211 retrocopy
retro_fcat_736,
Homo sapiens ENSG000000742012 retrocopies
retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla ENSGGOG000000030911 retrocopy
retro_ggor_2084,
Macropus eugenii ENSMEUG000000059354 retrocopies
retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus ENSMUSG000000254391 retrocopy
retro_mmus_1984,
Nomascus leucogenys ENSNLEG000000166992 retrocopies
retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus ENSOCUG000000243931 retrocopy
retro_ocun_1303,
Pongo abelii ENSPPYG000000037121 retrocopy
retro_pabe_2494,
Sorex araneus ENSSARG000000094602 retrocopies
retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus ENSSTOG000000279803 retrocopies
retro_itri_239, retro_itri_319, retro_itri_490,




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