RetrogeneDB ID: retro_btau_650

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:64776854..64777491(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

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

Sequence

>retro_btau_650
AGGAGAGAGCAAGAAAGGATTTGTCTCTTTTCTGTGGACCCTTATAATTTTGAAACTCAGGCAGAAATAGAAGATACAAG
GTAATAGCACATTGAAGAAAACATGGCAATAACTATGGAAGAGGCTCTGGAAAGTTTGGGCTGAGTAATGATGCTTTGTA
TTAACTGCGAAGTGAATGGACATCCTGTGAAATTGTTGGTTGACTCAGGTGCCCAGAGGATTATGACGGACCAAGCTCCT
GCAGAAAGCTGTAATATAATGAGGCTGGTGGACTATTGGTGGGCAGGGATGGCCAAAGGAATGGGCTCCCAGAAGATTAT
TGGAACGGTACATCTAGTTCAGGTTCAAAAGGAAGCAGATTTCCTGGCTTGTTCCTTCTCTATACTTTAGGAAGAGCCTG
TAGACATGCTTCCAGGACTGGATATGTTGAAATGGCATTGATGTTCCATTGACCTCAAGAAAAATGTACTCATGATGAGG
ACTACAGGCTCACAGACCATCTTCCTTCCTGAGGGAGAGTTACCAGAGTGTACCCCGTTGGCATATGGGGCCAGGTAAGA
GGCCAGAGGAGATTGCAGACCAAGAATTAGCAGAAGCCCTTCAGAAATCCATAGAAGATGCAGAGTGTCAGAATCCA

Alignment

ORF - retro_btau_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.35 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDS
          RREQERI.LFS.DP...E.QA.IE.D.R...IEENM.I.MEEA.ES.G.V.ML.INC.VNGHPVK..VDS
Retrocopy RREQERICLFSVDPYNFETQAEIE-DTR**HIEENMAITMEEALESLG*VMMLCINCEVNGHPVKLLVDS

Parental  GAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQPMDMLLG
          GAQ.....QA.AE.CNIMRLVD..WAG.AKG.G.QKIIG.VHL.QVQ.E.DFLACSFSIL.E.P.DML.G
Retrocopy GAQRIMTDQAPAESCNIMRLVDYWWAGMAKGMGSQKIIGTVHLVQVQKEADFLACSFSIL*EEPVDMLPG

Parental  LDMLKRHQCSIDLKKNVLVIGTTGSKTTFLPEGELPECARLAY-GAGRDEVRPEEIADQELAEALQKSVE
          LDMLK.H.CSIDLKKNVL...TTGS.T.FLPEGELPEC..LAY.G.G....RPEEIADQELAEALQKS.E
Retrocopy LDMLKWH*CSIDLKKNVLMMRTTGSQTIFLPEGELPECTPLAY>GPGK---RPEEIADQELAEALQKSIE

Parental  DAERQKP
          DAE.Q.P
Retrocopy DAECQNP

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	0.00 RPM	4.25 RPM
ERP005899_muscle	0.00 RPM	14.15 RPM
SRP017611_brain	0.00 RPM	3.70 RPM
SRP017611_kidney	0.00 RPM	11.56 RPM
SRP017611_liver	0.00 RPM	16.54 RPM
SRP030211_testis	0.02 RPM	1.52 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_650 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_650 has 0 orthologous retrocopies within eutheria group .

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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,