RetrogeneDB ID: retro_btau_227

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:35948786..35950742(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000010803
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CHM
• Ensembl ID: ENSBTAG00000009598
• Aliases: None
• Description: rab proteins geranylgeranyltransferase component A 1 [Source:RefSeq peptide;Acc:NP_001192318]

Sequence

>retro_btau_227
ATGGCCAACAGTCTCCCAACAGAATTTGATGTGATAGTGATGGGGACAGGTCTGCCTGAATCCATCCTTGCCGCTGCATG
TTCCAGAAGTGGTCAAAGGGTTCTGCATCTCGATTCAAGAAGTTACTATGGGGGAAACTGGGCTAGTTTCAGCTTTCCAG
GATTGCTATCCTGGTTGAAGGAACATCAGCAAAACAGTGACACTGGGGAGGAAAGCCCTGCTGCATGGCAAGACATGATC
CATGAAACAGAAGAAGCCATCCCTCTTTGCAAGAAGGATGAAACCATTCAACACGCCGAAGTTTTTTGTTATGCCAGTCA
GGGCATGGATGGCAATATTGAAGAGCTTGGTGCCCTGCAGAAAAATCCTTCTTGTGTAGCATCTAGTACCCTCATAAAAC
CTCTGGATTCTGCATGCTTGTCTGAGGAAACACACTCATCACACATTACTAGCTATGAAGTGCCTACACAAGACACTCCA
AAAAACAATGAAGAAATAACTGATACGGCAGAAACTTCTGTGAAAGAAGAATATTGTGGGTATGATACTTATAAACACAC
AGTTTCAGATGGCACTAAAGATGAAATCAAACCTGTACTGGAAGACAACAGTGTGCCACCAAAGAGAAAAAGGATTGCTT
ACTCTCAAATAGTTAAAGAAGGCAGGAGGTTTAATATTGATCTGTCATCGAAGCTGCTTTATTCTCAAGGACTGTTAATC
GATCTGTTAATCAAATCAAATGTTAGTCGTTACGCTGAATTTAAAAATGTCACTAGAATTCTTGCATTTCGAGAAGGAAA
AGTAGAGCAGGTGCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAAGAGCTCACTATGGTTGAAAAGAGGATGCTAATGA
AATTTCTTACATTTTGTTTAGATTATGAACAACATCCTGAGGAATACCAAGCTTTCACACAATGCTCATTTTCAGAGTAC
TTGAAAACCAAAAACTTAACCCCCAGCCTCCAGCATTTTATACTTCACTCGATTGCCATGATGTCAGAATCCTCTTGCAC
TACAGTAGATGGCCTTAAAGCAACAAAAACCTTTCTTCAGTGTCTTGGACGGTTTGGCAACACTCCCTTTTTATTTCCCT
TATATGGCCAAGGTGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTCGGTGGGATATATTGTCTTCGCCATAAA
GTACAATGCCTTGTAGTTGACAGAGAATCTGGAAGATGTAAAGCAATTATAGATCACCTTGGTCAAAGGATAAATGCTAA
ATATTTCATTGTGGAAGATAGTTACCTGTCTGAGGAAACATGTTCAAGTGTGCAGTACAAGCAGATATCCAGGGCAGTGC
TCATTACAGATCAGTCTGTCCTAAAGACAGATTCAGATCAGCAGATTTCCATTTTGATAGTACCTCCGGTGGAACCAGGA
GCACATGCTGTCCGAATCATTGAATTGTGTTCTTCAACCATGACATGCATGAAAGACACCTACCTGGTACATCTGACCTG
TTCATCTTCCAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTATTCACCCCATATTCTGAGACAGAAGTAG
ACAATGAAGAACTTCCAAAGCCAGGACTCTTGTGGGCTCTTTATTTTAACATGAGAGATTCCTCGGGAGTCAGCCGTAGC
TCATACAATGGCTTGCCTCCCAACGTTTATGTCTGCACTGGGCCTGACTCTGGACTCGGAAGTGAGCATGCCGTCAAGCA
AGCTGAAACACTCTTCCACGAGATCTTTCCAAGTGAAGAATTCTGCCCCCCACCTCCAAATCCGGAAGACATTTTCTTTG
ACGGTGATGAAAAGCCATCAGAGCCTCTTGGAACCAATAATATAGTAATGGCCAAACTAGAATCCTCTGAGGGAAGCAAA
AACCTAGAAAGTTCAGGGAAGCACCTTCAAAATTAG

Alignment

ORF - retro_btau_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSYYGGNWASFSFSGLLSWLKEHQENSDIVNECPA-WQEKIHENEEAIALSRTDKTIQHVEVFCYACQDL
          RSYYGGNWASFSF.GLLSWLKEHQ.NSD...E.PA.WQ..IHE.EEAI.L...D.TIQH.EVFCYA.Q..
Retrocopy RSYYGGNWASFSFPGLLSWLKEHQQNSDTGEESPAAWQDMIHETEEAIPLCKKDETIQHAEVFCYASQGM

Parental  HEDVEEAGALQKNHASVTSVNCTEAADSACLPVEDESLRTTSCEIPAEQTPSSDPERALEVNDVQVTGEK
          ....EE.GALQKN...V.S.......DSACL..E..S...TS.E.P...T....P....E..D...T..K
Retrocopy DGNIEELGALQKNPSCVASSTLIKPLDSACLSEETHSSHITSYEVPTQDT----PKNNEEITDTAETSVK

Parental  ENCCDDNTCVPSTAEKETSENVPVAEDTAEQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIK
          E..C...T...........E..PV.ED....PK..RI.YSQI.KEGRRFNIDL.SKLLYS.GLLIDLLIK
Retrocopy EEYCGYDTYKHTVSDGTKDEIKPVLEDNSVPPKRKRIAYSQIVKEGRRFNIDLSSKLLYSQGLLIDLLIK

Parental  SNVSRYAEFKNITRILAFREGRVKQVPCSRADVFNSKQLTMVEKRMLMKFLTFCMEYEEHPDEYKAYEEI
          SNVSRYAEFKN.TRILAFREG.V.QVPCSRADVFNSK.LTMVEKRMLMKFLTFC..YE.HP.EY.A....
Retrocopy SNVSRYAEFKNVTRILAFREGKVEQVPCSRADVFNSKELTMVEKRMLMKFLTFCLDYEQHPEEYQAFTQC

Parental  TFSEYLKTQKLTPNLQYFVLHSMAMTSETGSSTIDGLKATKNFLHSLGRYGNTPFLFPLYGQGELPQCFC
          .FSEYLKT..LTP.LQ.F.LHS.AM.SE....T.DGLKATK.FL..LGR.GNTPFLFPLYGQGE.PQCFC
Retrocopy SFSEYLKTKNLTPSLQHFILHSIAMMSESSCTTVDGLKATKTFLQCLGRFGNTPFLFPLYGQGEIPQCFC

Parental  RMCAVFGGIYCLRHSVQCLVVDKESGKCKAIIDQYGQRIISKHFLVEDSYLSENTCAHVQYRQISRAILI
          RMCAVFGGIYCLRH.VQCLVVD.ESG.CKAIID..GQRI..K.F.VEDSYLSE.TC..VQY.QISRA.LI
Retrocopy RMCAVFGGIYCLRHKVQCLVVDRESGRCKAIIDHLGQRINAKYFIVEDSYLSEETCSSVQYKQISRAVLI

Parental  TDRSVLKTDSDQQISILTVPAEEPGTFAVRVIELCSSTMTCMKGSYLVHLTCTSSKTAREDLEPVVQKLF
          TD.SVLKTDSDQQISIL.VP..EPG..AVR.IELCSSTMTCMK..YLVHLTC.SSKTAREDLE.VV.KLF
Retrocopy TDQSVLKTDSDQQISILIVPPVEPGAHAVRIIELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLF

Parental  TPYTETEIENEEIEKPRLLWGLYFNMRDSSDVNRNTYNDLPSNVYVCSGPDCALGNDNAVKQAEALFQQI
          TPY.ETE..NEE..KP.LLW.LYFNMRDSS.V.R..YN.LP.NVYVC.GPD..LG...AVKQAE.LF..I
Retrocopy TPYSETEVDNEELPKPGLLWALYFNMRDSSGVSRSSYNGLPPNVYVCTGPDSGLGSEHAVKQAETLFHEI

Parental  CPNEDFCPPPPNPEDIILDGDSLQPEASESSALPEASSETPKESSNLRN
          .P.E.FCPPPPNPEDI..DGD....E.........A..E....S.NL..
Retrocopy FPSEEFCPPPPNPEDIFFDGDEKPSEPLGTNNIVMAKLESSEGSKNLES

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	3.46 RPM	1.66 RPM
ERP005899_muscle	7.92 RPM	5.12 RPM
SRP017611_brain	12.15 RPM	7.31 RPM
SRP017611_kidney	15.35 RPM	8.89 RPM
SRP017611_liver	8.76 RPM	2.64 RPM
SRP030211_testis	2.37 RPM	0.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_227 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI539416	35950407	35950577	97.7	169	0	166

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_227 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_56
Pan troglodytes	retro_ptro_400
Gorilla gorilla	retro_ggor_488
Pongo abelii	retro_pabe_215
Macaca mulatta	retro_mmul_460
Mus musculus	retro_mmus_284
Rattus norvegicus	retro_rnor_981
Oryctolagus cuniculus	retro_ocun_893
Canis familiaris	retro_cfam_1873
Equus caballus	retro_ecab_36

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010190	1 retrocopy	retro_amel_733,
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Bos taurus	ENSBTAG00000009598	1 retrocopy	retro_btau_227 ,
Canis familiaris	ENSCAFG00000017406	1 retrocopy	retro_cfam_1873,
Equus caballus	ENSECAG00000019201	1 retrocopy	retro_ecab_36,
Felis catus	ENSFCAG00000030652	1 retrocopy	retro_fcat_1744,
Homo sapiens	ENSG00000188419	1 retrocopy	retro_hsap_56,
Gorilla gorilla	ENSGGOG00000022912	1 retrocopy	retro_ggor_488,
Loxodonta africana	ENSLAFG00000000523	1 retrocopy	retro_lafr_441,
Myotis lucifugus	ENSMLUG00000011286	1 retrocopy	retro_mluc_138,
Macaca mulatta	ENSMMUG00000016776	1 retrocopy	retro_mmul_460,
Monodelphis domestica	ENSMODG00000014364	1 retrocopy	retro_mdom_1776,
Mustela putorius furo	ENSMPUG00000001194	1 retrocopy	retro_mputfur_831,
Mus musculus	ENSMUSG00000025531	1 retrocopy	retro_mmus_284,
Nomascus leucogenys	ENSNLEG00000002762	1 retrocopy	retro_nleu_120,
Oryctolagus cuniculus	ENSOCUG00000012819	1 retrocopy	retro_ocun_893,
Pongo abelii	ENSPPYG00000020520	1 retrocopy	retro_pabe_215,
Pan troglodytes	ENSPTRG00000022071	1 retrocopy	retro_ptro_400,
Rattus norvegicus	ENSRNOG00000000161	1 retrocopy	retro_rnor_981,
Sarcophilus harrisii	ENSSHAG00000017568	1 retrocopy	retro_shar_127,
Ictidomys tridecemlineatus	ENSSTOG00000022111	1 retrocopy	retro_itri_870,
Vicugna pacos	ENSVPAG00000001963	1 retrocopy	retro_vpac_231,