RetrogeneDB ID: retro_btau_1504

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:94789733..94790480(-)
• Located in intron of: ENSBTAG00000010716

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSBTAG00000014316
• Aliases: HNRNPH3, HNRPH3
• Description: heterogeneous nuclear ribonucleoprotein H3 [Source:RefSeq peptide;Acc:NP_001193508]

Sequence

>retro_btau_1504
TTCTTTCAGGGGTTGGAAATCGTGCCAAATGGAATAACTCTGATGATGGACTACCACGGGAGAAGCACAGGGGAGGCCTT
CGTGCCTTTGCTTCAAAGAAAATAGCAGAAAATGCACTTGGGAAACACAAGGAAAGAATGAGGCCCAGGGCTATTGAGAA
CCTCAGAAGTAGCAGCAAGGAAATCAAAGGATTTTATGATCCACCAAGAAGTTTGCTGGGCCAACAACCAGGACCACACG
ATAGACCAATAGGAGGAAGAGGAAATTATTATGGAGCTGGGCATGCAAGCATGTATGACAGAATTCGATGAGAAGATGAT
GGGTATGATGGTGATTATGGAGGTTTTGATGACTATGGTGGCCACAGTGTTTATGGCTACGGAAATGATGCCTTTGATGA
CAGCATGAGCGATGGAAGAGGTATGGGAGGACATGGCTATGGGGGAGTTGGTGATACAAGTTCAGGTTTTCATGGTAGTC
ATTTTGTACATATGAGAGGACCACCTTTTCAGGCAACTGGAGATGACATTGCTAATTTCTTCTCACCACTAAATTCAATC
CAAATGCATACTGATATTGGAACTGATGGCAGGGCAACAGGAGAAGATGTAGAGTTTGTGACATATGAAGATGCAGTAGC
TACCATGTCCAAAGAGAAGAATAACACACAACATCAATACATTGAACTCTTCTTGAATCAAATTCATGGAAGGCGGCTCA
GGAATGGGAGGTTACGGCAGAGATGGA

Alignment

ORF - retro_btau_1504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 72.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFQGLEIVPNGITLTMDYQGRSTGEAFVQ-FASKEIAENALGKHKERIGHRYIEIFRSSRSEIKGFYDPP
          FFQGLEIVPNGITL.MDY.GRSTGEAFV..FASK.IAENALGKHKER...R.IE..RSS..EIKGFYDPP
Retrocopy FFQGLEIVPNGITLMMDYHGRSTGEAFVP<FASKKIAENALGKHKERMRPRAIENLRSSSKEIKGFYDPP

Parental  RRLLGQRPGPYDRPIGGRGGYYGAGRGSMYDRMRRGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDRMRDG
          R.LLGQ.PGP.DRPIGGRG.YYGAG..SMYDR.R...DGYDG.YGGFDDYGG...YGYGND.FDD.M.DG
Retrocopy RSLLGQQPGPHDRPIGGRGNYYGAGHASMYDRIR*EDDGYDGDYGGFDDYGGHSVYGYGNDAFDDSMSDG

Parental  RGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVT
          RGMGGHGYGG.GD.SSGFHG.HFVHMRG.PF.AT..DIANFFSPLN.I..H.DIG.DGRATGE.DVEFVT
Retrocopy RGMGGHGYGGVGDTSSGFHGSHFVHMRGPPFQATGDDIANFFSPLNSIQMHTDIGTDGRATGE-DVEFVT

Parental  HEDAVAAMSKDKNNMQHRYIELFLNSTPG-GGSGMGGSGMGG
          .EDAVA.MSK.KNN.QH.YIELFLN...G.GGSGMGG.G..G
Retrocopy YEDAVATMSKEKNNTQHQYIELFLNQIHG>GGSGMGGYGRDG

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	86.95 RPM
ERP005899_muscle	0.00 RPM	66.46 RPM
SRP017611_brain	0.00 RPM	99.49 RPM
SRP017611_kidney	0.06 RPM	115.34 RPM
SRP017611_liver	0.00 RPM	34.73 RPM
SRP030211_testis	0.00 RPM	177.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1504 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1504 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504 , retro_btau_470,
Bos taurus	ENSBTAG00000020513	1 retrocopy	retro_btau_42,
Bos taurus	ENSBTAG00000021838	1 retrocopy	retro_btau_847,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,