RetrogeneDB ID:

retro_btau_1689

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:9:101442939..101443958(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000016421
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GHITM
Ensembl ID:ENSBTAG00000032829
Aliases:None
Description:growth hormone-inducible transmembrane protein [Source:RefSeq peptide;Acc:NP_001029224]


Retrocopy-Parental alignment summary:






>retro_btau_1689
GCTGGCCGCAAGACTTGTGTGTCTCCGAGCTCTACCTTCCAGGGTTTCACCAAGGCCTCCCCTGTTGTGAAGAATTCCAT
CACGAAGAATCAATGGCTTTTGACACCCAGCAGGGAGTATGCTACCAAGACAAGAATTGGGATTCGACGTGGAAAAGCAA
CCCAAGAACTCAAGGAGGCAGCTTTGGAACCATCCGTGGAAAAAATATTTAAAATTGATCAGATGGGAAGATGGTTTATT
GCTGGAGGGGCTGCAGTTGGTCTTGGAGCTTTGTGCTACTACGGATTGGGAATGTCTAATGAGATCAGAGCTATTGAAAA
AGCTGTAATGTGGCCTCAGTATGTGAAGGACAGAATTCATTCCACTTACATGTACTTAGCAGGAAGTATTGGCTTAACAG
CTTTGTCTGCCGTGGCAGTGAGCAGAACTCCTGCTCTCATGAACTTCATGATGAGAGGCTCTTGGATAACCATTGGTGCA
ACCTTTGCAGCCATGATTGGAGCTGGAATGCTGGTACAGTCAATATCATATGAGCAGAGTCCAGGCCCAAAGCACCTTGC
TTGGTTACTACATTCTGGTGTGATGGGTGCTGTGGTGGCTCCTCTGACGATACTAGGGGGGCCTCTTCTCCTCAGAGCTG
CGTGGTACACGGCTGGCATCGTGGGAGGTCTCTCCACCGTGGCCATGTGTGCGCCCAGTGAGAAGTTTCTCAACATGGGG
GCCCCCCTGGGTGTGGGCCTCGGTGTCGTCTTTGTGTCCTCACTAGGATCAATGTTCCTCCACCTACCACTGTGGCTGGT
GCCACTCTGTACTCAGTGGCGGTTTATGGTGGATTAGTTCTTTTCAGCATGTTTCTTCTATATGATACACAGAAAGTAAT
CAAGCGTGCAGAAGTAGTACCAATGTATGGAGTTCAGAAATACGACCCCATCAGTTCGATGCTGGGAATCGACATGGATA
CATTAAACATATTTATGCGTGTTGCCACTGTTCTAGCAACTGGAGGCAACAGGAAGAAG

ORF - retro_btau_1689 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.48 %
Parental protein coverage: 99.42 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAARLVCLRALPSRVFHPAFTKASPVVKNSITKNQWLLTPSREYATKTRIGIRRGKTTQELKEAALEPSVE
A.R..C....PS..F...FTKASPVVKNSITKNQWLLTPSREYATKTRIGIRRGK.TQELKEAALEPSVE
RetrocopyAGRKTCVS--PSSTFQ-GFTKASPVVKNSITKNQWLLTPSREYATKTRIGIRRGKATQELKEAALEPSVE
ParentalKIFKIDQMGRWFIAGGAAVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAGSIGLTALSA
KIFKIDQMGRWFIAGGAAVGLGALCYYGLGMSNEI.AIEKAV.WPQYVKDRIHSTYMYLAGSIGLTALSA
RetrocopyKIFKIDQMGRWFIAGGAAVGLGALCYYGLGMSNEIRAIEKAVMWPQYVKDRIHSTYMYLAGSIGLTALSA
ParentalVAVSRTPALMNFMMRGSWITIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTILGG
VAVSRTPALMNFMMRGSWITIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTILGG
RetrocopyVAVSRTPALMNFMMRGSWITIGATFAAMIGAGMLVQSISYEQSPGPKHLAWLLHSGVMGAVVAPLTILGG
ParentalPLLLRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGVVFVSSLGSMFL-PPTTVAGATLYSVAVY
PLLLRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGVVFVSSLGSMFL.PPTTVAGATLYSVAVY
RetrocopyPLLLRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGVVFVSSLGSMFL<PPTTVAGATLYSVAVY
ParentalGGLVLFSMFLLYDTQKVIKRAEVVPMYGVQKYDPINSMLGIYMDTLNIFMRVATILATGGNRKK
GGLVLFSMFLLYDTQKVIKRAEVVPMYGVQKYDPI.SMLGI.MDTLNIFMRVAT.LATGGNRKK
RetrocopyGGLVLFSMFLLYDTQKVIKRAEVVPMYGVQKYDPISSMLGIDMDTLNIFMRVATVLATGGNRKK

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 .00 RPM 309 .44 RPM
ERP005899_muscle 0 .26 RPM 125 .43 RPM
SRP017611_brain 0 .82 RPM 232 .37 RPM
SRP017611_kidney 1 .07 RPM 504 .88 RPM
SRP017611_liver 0 .53 RPM 207 .35 RPM
SRP030211_testis 0 .70 RPM 337 .12 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_1689 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1689 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1689 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097531 retrocopy
retro_amel_336,
Bos taurus ENSBTAG00000032829 2 retrocopies
retro_btau_1689 , retro_btau_779,
Choloepus hoffmanni ENSCHOG000000015761 retrocopy
retro_chof_5,
Cavia porcellus ENSCPOG000000064321 retrocopy
retro_cpor_1436,
Dasypus novemcinctus ENSDNOG000000188805 retrocopies
retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii ENSDORG000000011091 retrocopy
retro_dord_184,
Echinops telfairi ENSETEG000000017961 retrocopy
retro_etel_68,
Loxodonta africana ENSLAFG000000096461 retrocopy
retro_lafr_388,
Macropus eugenii ENSMEUG000000098613 retrocopies
retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus ENSMICG000000116211 retrocopy
retro_mmur_692,
Monodelphis domestica ENSMODG000000016933 retrocopies
retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus ENSOCUG000000060931 retrocopy
retro_ocun_260,
Otolemur garnettii ENSOGAG000000121201 retrocopy
retro_ogar_1287,
Rattus norvegicus ENSRNOG000000139611 retrocopy
retro_rnor_2461,
Sus scrofa ENSSSCG000000103451 retrocopy
retro_sscr_1102,
Tupaia belangeri ENSTBEG000000163652 retrocopies
retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta ENSTSYG000000063671 retrocopy
retro_tsyr_4,
Drosophila melanogaster FBgn00302631 retrocopy
retro_dmel_61,


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