RetrogeneDB ID:

retro_btau_913

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:20:5670193..5671459(-)
Located in intron of:ENSBTAG00000000564
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:STIP1
Ensembl ID:ENSBTAG00000015663
Aliases:None
Description:Stress-induced-phosphoprotein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBZ8]


Retrocopy-Parental alignment summary:






>retro_btau_913
ATGGAGCAGGTAAATGAGCTCAACAAGAAGGGCAACGAGGCCCTGAGAGCTGGCAACACTGACGATGCGCTACAGTGCTA
CTCTGAAGCCATTAAGTTAGACCCCCAGAACCATGTGCTCCGCAGCAATCGCTCAGCGGCCTATGCCAAGAAAGGAGACT
ACCAGAAGGCTTATGAGGACAGCTGCAAAACCACTGACCTAAAGCCTGACTGGGGCAAGGGCTATTCACGAAAAGCAGCA
GCTCTTGAATTCTTAAACCGATTTGAAGAAGCCAAGCAAACCTATGAGGAGGGTTTAAAACATGAAGCAAACAATCCTCA
GTTCAAAGAAGGTTTACAGAATATGGAGGCCCGGTTGGCAGAAAGGAAATTCATGAACCCTTTCAACATGCCTAATCTGT
ACCAGAAGTTGGAGAGTGGTCCCAGGACCAAGACTCTGCTTGCAGATCCTACCTACCGGGAACTGATCGAGCAGCTGCAG
AACAAGCCCTCCAACCTGGGCACGAAACTGCAAGATCCCTAGATCATGACTACTCTTAGCATCCTGCTCGGAGTTAATCT
GGGCAGTATGGATGAAGAGGAGGAAGTTGCAACACCTCTGCCACCACCTCCCCCCAAAAAGGAGACAAAACCAGAGCCAA
TGGAAGAAGATCTTCCAGAGAATAAGAAGCAGACGCTGAAAGAAAAAGAGCTGGGGAATGAAGCCTATAAGAAGAAGGTC
TTTGACACAGCCTTGAAGCACTACGACAGAGCCAAGGACCTGGATCCCACCAACATGACTCACATAACCCACCAAGCAGC
CGTGTACTTCGAGAAGGGTGACTATGGTCAATGCTGGGAGCTTAGTGAGGAGGCCATTGAAGTGGGGCGACAAAACCGAG
AAGACTACCGACAGATTGCCAAAGCTTATGCACTAATTGGCAACTCTTATTTCAAAGAAGAAAAGTACAAGGATGCCATC
CATTTCTATAACAAGTCTCTGGCAGAGCACCGAACCCCAGTTGTGGTCAAGAAATGCCAACAGGCAGAGAAAATCTTGAA
GGAGCAAGAGCGGCTGGCCTACATAAATCCTGACCTGGCCTTGGAGGAGAAGAACAAAGGCAATGAGTGTTTTCAGAAAG
GGGACTACTCCCAGGCCATGAAGCACTACAGAGAAGCCATCAAACGGAACCCCGAAGATGCCAAACTGTACAGCAACCGA
GCTGCCTGCTTCACCAAGCTCCTGGAGTTCCAGCTGGCGCTCAAGGACTGTGAGGAGTGGAGCCAA

ORF - retro_btau_913 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.71 %
Parental protein coverage: 77.72 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD
MEQVNEL..KGN.AL.AGN.DDALQCYSEAIKLDPQNHVL.SNRSAAYAKKGDYQKAYED.CKT.DLKPD
RetrocopyMEQVNELNKKGNEALRAGNTDDALQCYSEAIKLDPQNHVLRSNRSAAYAKKGDYQKAYEDSCKTTDLKPD
ParentalWGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLESD
WGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQ.KEGLQNMEARLAERKFMNPFNMPNLYQKLES.
RetrocopyWGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQFKEGLQNMEARLAERKFMNPFNMPNLYQKLESG
ParentalPRTKTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPPKKETK
PRTKTLLADPTYRELIEQL.NKPS.LGTKLQDP.IMTTLS.LLGV.LGSMDEEEEVATP.PPPPPKKETK
RetrocopyPRTKTLLADPTYRELIEQLQNKPSNLGTKLQDP*IMTTLSILLGVNLGSMDEEEEVATPLPPPPPKKETK
ParentalPEPMEEDLPENKKQALREKELGNEAYKKKDFDTALKHYDKAKDLDPTNMTYITNQAAVYFEKGDYGQCRE
PEPMEEDLPENKKQ.L.EKELGNEAYKKK.FDTALKHYD.AKDLDPTNMT.IT.QAAVYFEKGDYGQC.E
RetrocopyPEPMEEDLPENKKQTLKEKELGNEAYKKKVFDTALKHYDRAKDLDPTNMTHITHQAAVYFEKGDYGQCWE
ParentalLCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQE
L.E.AIEVGR.NREDYRQIAKAYA.IGNSYFKEEKYKDAIHFYNKSLAEHRTP.V.KKCQQAEKILKEQE
RetrocopyLSEEAIEVGRQNREDYRQIAKAYALIGNSYFKEEKYKDAIHFYNKSLAEHRTPVVVKKCQQAEKILKEQE
ParentalRLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEEC
RLAYINPDLALEEKNKGNECFQKGDY.QAMKHY.EAIKRNP.DAKLYSNRAAC.TKLLEFQLALKDCEE.
RetrocopyRLAYINPDLALEEKNKGNECFQKGDYSQAMKHYREAIKRNPEDAKLYSNRAACFTKLLEFQLALKDCEEW
ParentalIQ
.Q
RetrocopySQ

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 23 .50 RPM
ERP005899_muscle 0 .00 RPM 101 .88 RPM
SRP017611_brain 0 .00 RPM 94 .05 RPM
SRP017611_kidney 0 .00 RPM 73 .02 RPM
SRP017611_liver 0 .00 RPM 39 .87 RPM
SRP030211_testis 0 .02 RPM 133 .55 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_913 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_913 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_913 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000015663 2 retrocopies
retro_btau_836, retro_btau_913 ,
Canis familiaris ENSCAFG000000146726 retrocopies
retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus ENSCJAG000000182092 retrocopies
retro_cjac_1043, retro_cjac_2222,
Cavia porcellus ENSCPOG000000029141 retrocopy
retro_cpor_1443,
Felis catus ENSFCAG000000059371 retrocopy
retro_fcat_1510,
Homo sapiens ENSG000001684391 retrocopy
retro_hsap_4867,
Gorilla gorilla ENSGGOG000000121321 retrocopy
retro_ggor_3040,
Microcebus murinus ENSMICG000000169331 retrocopy
retro_mmur_1045,
Macaca mulatta ENSMMUG000000129531 retrocopy
retro_mmul_2607,
Nomascus leucogenys ENSNLEG000000047771 retrocopy
retro_nleu_2000,
Pan troglodytes ENSPTRG000000038201 retrocopy
retro_ptro_3242,
Rattus norvegicus ENSRNOG000000211642 retrocopies
retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus ENSSTOG000000142621 retrocopy
retro_itri_1578,
Tursiops truncatus ENSTTRG000000102351 retrocopy
retro_ttru_1900,




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