RetrogeneDB ID:

retro_btau_1185

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:29:2492227..2493302(-)
Located in intron of:ENSBTAG00000004081
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.20352
Ensembl ID:ENSBTAG00000002608
Aliases:None
Description:septin-2 [Source:RefSeq peptide;Acc:NP_001039557]


Retrocopy-Parental alignment summary:






>retro_btau_1185
ATGTCTAAGGAACAACCAACTCCATTTATAAATCCAGAAACTCCTGGATATGTTGGATTTGCAAACCTTCCCAAATCAAG
TTCATCGAAAATCAGTGAAAAAAGGTTTTGAATTCACACTAGTGGTGGTCGGTGAATTGGGTCTCATAAAATCGATGCTC
ATAAACCTCATCTTGCTGACTGACCTCTACCCAGAAAGAGTCTTACCTGGAGCTGCAAAGAAAATTGCAAGAACTCTTCA
AATTGAGGCTTCAACTGTTGAAACTGAAGAGCAAGGATCAAGCTGCGTCTGACCATGCTGGACGCACCGGGCTTCGGGAA
CACCATCAACTGCAGGGACTGCTTTAAAACAGTCATCTCCTACATCGATGGCAGTTTGAACAGTGCCTGCAGGATGAGAG
TGGTCTGAGCAGAGGCGCATCATCAGTAACAGGGTGCACTGCTGCTTTTACCTCATTTCCCCTTTCAGACACAGACTTCA
GCCGTTGGATGTTGCGTTTGTGAAGGCAATACACAGCAAGGTGAACACTGTGCCTGTCGTTGAGAAAGGCTACATGCGCA
CACTGAAGGAGCAGGAGCACCTGAAGAAAAGGATTCTGGATGAAATCGAGAAACATGACATCAGAATCTATCACTTACCT
GATGCAGAGTCTGGTGAAGATGAAGATTTCAAAGAGCAGACTAGACTTCTCAAGAGCAGCATCCCTTTCTCTGTGGTTGG
ATCCAATCAGCTGATTGAAGCCCAAGGCAAGAAGGTCAGAGGCCGCCTCTACCCTTGGGGCATCCTGGAGGTGGAGAACC
TGGAGCACAAGGACTTTCTGAAGCTGAGGACGACGCTCATCACTCACGTGCAGGATCTCCAAGAGGTGACCCAGGACCTT
CACTATGAGAACTTCTGATCAGAGAGGCTCAAGAGAGGTGGCAGAAAGGTGGAAAATGAGGACATGAATAAAGACCAGAT
TTTTCTGGAAAAGGAAGCTGAGTTCCACCACATGCAAGAGATGATCACCTCGATGAAGGGGCAGCTGTAGCTGCAGGGCA
GCGACAGTGATGGCAAGATCCACGGGCAGCACGTG

ORF - retro_btau_1185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.89 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMSKQQQTQFINPETPGYVGFANLP-NQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERVIP
MSK.Q.T.FINPETPGYVGFANLP.NQVHRKSVKKGFEFTL.VVGE.GL.KS.LIN...LTDLYPERV.P
RetrocopyMSKEQPTPFINPETPGYVGFANLP>NQVHRKSVKKGFEFTLVVVGELGLIKSMLINLILLTDLYPERVLP
ParentalGAAEKIERTVQIEASTVEIEERG-VKLRLTVVDTPGYGDAINCRDCFKTIICYIDE-QFERYLHDESGLN
GAA.KI.RT.QIEASTVE.EE.G..KLRLT..D.PG.G..INCRDCFKT.I.YID..QFE..L.DESGL.
RetrocopyGAAKKIARTLQIEASTVETEEQG<IKLRLTMLDAPGFGNTINCRDCFKTVISYIDG<QFEQCLQDESGLS
ParentalR-RHIIDNRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKADSLKRMALKRVKYHILDEIEEH
R.R.II.NRVHCCFY.ISPF.H.L.PLDVAF.KAIH.KVN.VPV..K............K..ILDEIE.H
RetrocopyR<RRIISNRVHCCFYLISPFRHRLQPLDVAFVKAIHSKVNTVPVVEKGYMRTLKEQEHLKKRILDEIEKH
ParentalNIKIYHLPDAESDEDEDFKEQTRLLKASIPFSVVGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKL
.I.IYHLPDAES.EDEDFKEQTRLLK.SIPFSVVGSNQLIEA.GKKVRGRLYPWG..EVEN.EH.DFLKL
RetrocopyDIRIYHLPDAESGEDEDFKEQTRLLKSSIPFSVVGSNQLIEAQGKKVRGRLYPWGILEVENLEHKDFLKL
ParentalRTMLITHMQDLQEVTQDLHYENFRSERLKRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQLQ
RT.LITH.QDLQEVTQDLHYENF.SERLKRGGRKVENEDMNKDQI.LEKEAE...MQEMI..M....QL.
RetrocopyRTTLITHVQDLQEVTQDLHYENF*SERLKRGGRKVENEDMNKDQIFLEKEAEFHHMQEMITSMKG--QL*
ParentalLQGGDGDSGVHGQHV
LQG.D.D...HGQHV
RetrocopyLQGSDSDGKIHGQHV

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 13 .27 RPM
ERP005899_muscle 0 .00 RPM 53 .79 RPM
SRP017611_brain 0 .23 RPM 77 .61 RPM
SRP017611_kidney 0 .12 RPM 78 .00 RPM
SRP017611_liver 0 .08 RPM 35 .49 RPM
SRP030211_testis 0 .02 RPM 153 .29 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_1185 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1185 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1185 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000002608 1 retrocopy
retro_btau_1185 ,
Bos taurus ENSBTAG000000042911 retrocopy
retro_btau_627,
Canis familiaris ENSCAFG000000129601 retrocopy
retro_cfam_1477,
Choloepus hoffmanni ENSCHOG000000087155 retrocopies
retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus ENSCJAG000000061221 retrocopy
retro_cjac_1501,
Cavia porcellus ENSCPOG000000136871 retrocopy
retro_cpor_845,
Loxodonta africana ENSLAFG000000119641 retrocopy
retro_lafr_4,
Macropus eugenii ENSMEUG000000165191 retrocopy
retro_meug_39,
Myotis lucifugus ENSMLUG000000071081 retrocopy
retro_mluc_1594,
Monodelphis domestica ENSMODG000000160411 retrocopy
retro_mdom_888,
Mustela putorius furoENSMPUG000000001661 retrocopy
retro_mputfur_436,
Nomascus leucogenys ENSNLEG000000138731 retrocopy
retro_nleu_1848,
Otolemur garnettii ENSOGAG000000044571 retrocopy
retro_ogar_2239,
Pteropus vampyrus ENSPVAG000000005581 retrocopy
retro_pvam_448,
Rattus norvegicus ENSRNOG000000179521 retrocopy
retro_rnor_1110,
Ictidomys tridecemlineatus ENSSTOG000000133571 retrocopy
retro_itri_1227,
Drosophila melanogaster FBgn00117101 retrocopy
retro_dmel_35,


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