RetrogeneDB ID:

retro_btau_1474

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:6:1462255..1462933(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.64559
Ensembl ID:ENSBTAG00000013631
Aliases:None
Description:Glutamine synthetase [Source:UniProtKB/Swiss-Prot;Acc:P15103]


Retrocopy-Parental alignment summary:






>retro_btau_1474
GCCACCTCGGTCAGCTCCCACTTGGACAAAGCCATCAGCCAGGTGTACATGGCCCTACCTCAGGGCAAGAAAGTCCAAAC
TATGTATATCTGGATCGACGGTACTGCAGAAGGACTGTGCTGTAAGACCTGAACCTCGGATTCTGAGCCCAAGTGCATAG
AAGAGTTGCCTGACTGAAATTTGGATGGCTCTAGGACTTTTAGGTCTGAAGGCTCCAACAGTGACATGTATCTTGTCCCT
CCTGCCATGTTTTGGGACCCTTTCTGCAAGGACCCCAACAAGCTGGTGTTCTGTGAAGTCTTCAAGTACAACCCCAAAGC
CTGCAGAGACCAATTTATGGCACCCCTGTAAATGGATAATGGACATGGTGAGCAACCAGCACCCCTGGTTTGAAATGAAG
CAGGAATGTACCCTCAGGGGCACAGAAGGCTCCTCTTTGGTTGGCCTTCCAATGGCTCTCCTGGGCCCCAAGGTCCATAC
TACTGCAGTGTGGGAGAGGACAAGGCCTACGGCAGGGACATTGTGGAGGCTCACTGCCAGGCCTGCTTGTATGCTGGCAT
CAAGATCAGGGGCACAGACACCAAAGCCATGCCTGTGCAGTGGAGATTCCAGTTAGGGCCCTGTGCAGGAGTCAATGTGG
GAGATCGTCTCTGGGCAGCCCGCTTCATCTTGCACAGG

ORF - retro_btau_1474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.63 %
Parental protein coverage: 60.59 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalATSASSHLNKGIKQVYMALPQGDKVQAMYIWIDGTGEGLRCKTRTLDSEPKCIEELPEWNFDGSSTFQSE
ATS.SSHL.K.I.QVYMALPQG.KVQ.MYIWIDGT.EGL.CKT.T.DSEPKCIEELP..N.DGS.TF.SE
RetrocopyATSVSSHLDKAISQVYMALPQGKKVQTMYIWIDGTAEGLCCKT*TSDSEPKCIEELPD*NLDGSRTFRSE
ParentalGSNSDMYLVPAAMFRDPFRKDPNKLVFCEVFKYN-RKPAETNLRHTCKRIMDMVSNQRPWFGMEQEYTLM
GSNSDMYLVP.AMF.DPF.KDPNKLVFCEVFKYN..KPAETNL.H.CK.IMDMVSNQ.PWF.M.QE.TL.
RetrocopyGSNSDMYLVPPAMFWDPFCKDPNKLVFCEVFKYN>PKPAETNLWHPCKWIMDMVSNQHPWFEMKQECTLR
ParentalGTDGHP-FGWPSNGFPGPQGPYYCGVGADKAYGRDIVEAHYRACLYAGIKIGGTNAEVMPAQWEFQIGPC
GT.G...FGWPSNG.PGPQGPYYC.VG.DKAYGRDIVEAH..ACLYAGIKI.GT....MP.QW.FQ.GPC
RetrocopyGTEGSS<FGWPSNGSPGPQGPYYCSVGEDKAYGRDIVEAHCQACLYAGIKIRGTDTKAMPVQWRFQLGPC
ParentalEGIDMGDHLWVARFILHR
.G...GD.LW.ARFILHR
RetrocopyAGVNVGDRLWAARFILHR

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 97 .19 RPM
ERP005899_muscle 0 .00 RPM 105 .05 RPM
SRP017611_brain 0 .05 RPM 2225 .86 RPM
SRP017611_kidney 0 .00 RPM 357 .59 RPM
SRP017611_liver 0 .00 RPM 226 .53 RPM
SRP030211_testis 0 .00 RPM 456 .19 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_1474 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1474 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1474 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000013631 4 retrocopies
retro_btau_1050, retro_btau_1474 , retro_btau_336, retro_btau_824,
Canis familiaris ENSCAFG000000131022 retrocopies
retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus ENSCJAG000000046541 retrocopy
retro_cjac_2837,
Dasypus novemcinctus ENSDNOG000000139484 retrocopies
retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus ENSECAG000000158651 retrocopy
retro_ecab_979,
Echinops telfairi ENSETEG000000083293 retrocopies
retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus ENSFCAG000000105511 retrocopy
retro_fcat_1811,
Homo sapiens ENSG000001358214 retrocopies
retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla ENSGGOG000000247123 retrocopies
retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana ENSLAFG000000007001 retrocopy
retro_lafr_196,
Macropus eugenii ENSMEUG000000017746 retrocopies
retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta ENSMMUG000000228842 retrocopies
retro_mmul_2047, retro_mmul_954,
Monodelphis domestica ENSMODG000000067874 retrocopies
retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus ENSMUSG000000264733 retrocopies
retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys ENSNLEG000000180073 retrocopies
retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii ENSPPYG000000004401 retrocopy
retro_pabe_2698,
Pan troglodytes ENSPTRG000000017514 retrocopies
retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii ENSSHAG000000001161 retrocopy
retro_shar_553,
Sus scrofa ENSSSCG000000155451 retrocopy
retro_sscr_726,
Ictidomys tridecemlineatus ENSSTOG000000145292 retrocopies
retro_itri_1083, retro_itri_743,
Tupaia belangeri ENSTBEG000000035223 retrocopies
retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta ENSTSYG000000020661 retrocopy
retro_tsyr_385,
Tursiops truncatus ENSTTRG000000107811 retrocopy
retro_ttru_543,