RetrogeneDB ID: retro_btau_15

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:4642727..4643918(-)
• Located in intron of: ENSBTAG00000034827

Retrocopy information

• Ensembl ID: ENSBTAG00000002887
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSBTAG00000018718
• Aliases: DDI2, RSC1A1
• Description: None

Sequence

>retro_btau_15
ATGCTGCTCACGGTCTACTGCGTGCGGAGGGACCTCTCCGAGGCCACCTTCTCCCTGCAGGTCAGGCCCGACTTTGAACT
TCACAACTTCCGTGTGCTCTGTGAGCTGGAGTCCGGCATCCCTGCCGAGGAGACCCAGATAGTCTACATGGAGCGGCTTC
TCGTCAACGACCACTGCTCCCTGGGCTCCTACGGCCTCAAGGACGGCGACATGGTCATTTTACTGCAGAAGGAGGCCATG
CGGCCGCGCTCCCCAGAGCGGGCGGCCGGCCTGTGCAGCATGGAACCGGCGGGGCCCGCCCTACCCGGGACGTCCGGCTC
CCGGCCGCACCAGCGCGCCCAGTCGGCCCAGCACTCCAGCCGCCGCGGCTCTGGGGAGAAGGCGGGCCCGGGTCAAGGGC
TAGACAGCCCGGCCCTGGTCCGGAGCATGCTCCTGTCCAGCCCACACGACCTGTCCCTGCTGAAAGAGCGCAACCCTTCC
CTGGCTGAAGCGCTGCTCAGCGGAAACCTGGAGAGCTTCTCCCAGGTCCTGATGGAGCAGCAAAGGGAGAGGGCGCTGAG
AGAGCAAGAGCGACTGCGCCTCTTCTCCGCTGACCCGTTCGATCTGGAGGCCCAAGCCAAGATAGAGGAGGAGATCCGGC
AGCAGAACATCGAGGAGAACATGAGCATAGCCATGGAAGAGGCGCCGGAGAGCTTCGGCCAGGTGGCTATGCTCTACATC
AACTGCAGAGTCAACGGGCATCCTCTGAAGGCTTTCGTCGACTCGGGGGCCCAGATGACCATCATGAACCAAGTCTGTGC
CGAGAGATGCAACATCATACGGCTGGTGGATCGGCGGTGGGCCGGGGTCGCTAAAGGCGTGGGCACGCAGCGAATTCTCG
GCCGAGTCCACCTAGCGCAGATTCAGATCGAAGGCGACTTCTTACAGTGCTCTTTCTCTATACTGGAGGAGCAGCCCATG
GACATGCTTCTTGGGCTGGATATGCTCAGGAGACATCAGTGTTCCATCGACCTTAAGAGAAACGTGCTGGTGATCGGCAC
AACTGGCACACAGACTTCCTTCCTTCCTGAGGGAGAGTTACCTCCATGTGCTAAGTTGGTAAGTGGGATGGGGCCAGAGG
AGTCTTCAGATAAGGAAACAGCAAATGCTATTAAACATTCAGTCATGGATTCGGGGCGGAAAAAGCATTGA

Alignment

ORF - retro_btau_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.82 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLTVYCVRRDLSEVTFSLQVDADFELHNFRALCELESGIPAAESQIVYAERPLTDNHRSLASYGLKDGD
          MLLTVYCVRRDLSE.TFSLQV..DFELHNFR.LCELESGIPA.E.QIVY.ER.L...H.SL.SYGLKDGD
Retrocopy MLLTVYCVRRDLSEATFSLQVRPDFELHNFRVLCELESGIPAEETQIVYMERLLVNDHCSLGSYGLKDGD

Parental  VVILRQKENADPRPSVQFPNLPRIDFRSIAVPGTSNTR--QRQPPGVQQSHSAPGEIASSPQGLDNPALL
          .VIL.QKE...PR.......L........A.PGTS..R..QR.......S....GE.A...QGLD.PAL.
Retrocopy MVILLQKEAMRPRSPERAAGLCSMEPAGPALPGTSGSRPHQRAQSAQHSSRRGSGEKAGPGQGLDSPALV

Parental  RDMLLANPHELSLLKERNPPLADALLSGDLERFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAKIEE
          R.MLL..PH.LSLLKERNP.LA.ALLSG.LE.FS.VL.EQQ..RA.REQER.RLFSADPFDLEAQAKIEE
Retrocopy RSMLLSSPHDLSLLKERNPSLAEALLSGNLESFSQVLMEQQRERALREQERLRLFSADPFDLEAQAKIEE

Parental  DIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRLVDRRW
          .IRQQNIEENM.IAMEEAPESFGQV.MLYINC.VNGHP.KAFVDSGAQMTIM.Q.CAERCNI.RLVDRRW
Retrocopy EIRQQNIEENMSIAMEEAPESFGQVAMLYINCRVNGHPLKAFVDSGAQMTIMNQVCAERCNIIRLVDRRW

Parental  AGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQPMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGS
          AG.AKGVGTQ.I.GRVHLAQ.QIEGDFL.CSFSILEEQPMDMLLGLDML.RHQCSIDLK.NVLVIGTTG.
Retrocopy AGVAKGVGTQRILGRVHLAQIQIEGDFLQCSFSILEEQPMDMLLGLDMLRRHQCSIDLKRNVLVIGTTGT

Parental  KTTFLPEGELPECARLAYGAGRDEVRPEEIAD
          .T.FLPEGELP.CA.L..G.G..E....E.A.
Retrocopy QTSFLPEGELPPCAKLVSGMGPEESSDKETAN

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	0.07 RPM	4.25 RPM
ERP005899_muscle	0.05 RPM	14.15 RPM
SRP017611_brain	0.05 RPM	3.70 RPM
SRP017611_kidney	0.06 RPM	11.56 RPM
SRP017611_liver	0.00 RPM	16.54 RPM
SRP030211_testis	87.73 RPM	1.52 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_15 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_15 has 11 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_96
Pan troglodytes	retro_ptro_570
Gorilla gorilla	retro_ggor_143
Pongo abelii	retro_pabe_158
Macaca mulatta	retro_mmul_231
Callithrix jacchus	retro_cjac_196
Mus musculus	retro_mmus_67
Oryctolagus cuniculus	retro_ocun_249
Sus scrofa	retro_sscr_6
Canis familiaris	retro_cfam_193
Equus caballus	retro_ecab_110

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15 , retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,