RetrogeneDB ID: retro_btau_552

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:75849992..75850801(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000032281
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSBTAG00000004256
• Aliases: None
• Description: Ornithine decarboxylase [Source:UniProtKB/Swiss-Prot;Acc:P27117]

Sequence

>retro_btau_552
CTTTTGGAACGGGCGAAAGAGCTAGGTATTGATGTCATTGGTGTCAGCTTCCACGTGGGAAGTGGCTGTACTGATCCTGA
GACCTTTGTGCAGGCCATCTCTGATGCCCGCTGTGTCTTTGACATGGGCGCTGAGGTTGGTTTCAACATGTATCTGCTTG
AAATTGGTGGTGGCTTTCCTGGATCCGAGGATGTAAAGCTTAAATTTGAAGAGATCACCAATGTAATCAACCCAGCACTG
GACAAGTATTTTCCATCAGACTCTGGAGCGAGAATCATAGCTGAGCCTGGCAGATACTATGTTGCATCAGCTTTCACGCT
CGCAGTTAATATCATTGCCAAAAAACTTGTATTAAAGGAACAGACAGGTTCTGATGACGAAGAGGAGTCAAGTGAATGGA
CATTTATGTATTACGTGAACGATGGAGTATATGGGTCATTCAACTGTATCCTTTACGATCATGCACACGTGAAGCCTCTT
CTGCAGAAGAGACCCAAATCAGATGAGAAGTATTATTCATCCAGCATCTGGGGACCGACCTGTGACGGCCTGGACCGCAT
TGTTGAGCGCTGTAACCTGCCCGAGATGCATGTGGGTGATTGGATGCTCTTTGAGAACATGGGTGATTACACTGTTACTG
CTGCTTCTACCTTCAATGGATTCCAGAGACCCACCATCTACTATGTGATGTCAGGGCCAACATGGCAACTGATGCAGCAG
ATCCGGACCCAGGAATTCCGCCCAGAGTGGAGGAGCCAGACGTCGGTCTCCTGCCCATGTCCTGTGCCCAGGAGAGCGGC
ACTCGGCAG

Alignment

ORF - retro_btau_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 58.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLERAKELDIDVIGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFNMYLLDIGGGFPGSEDVKLKFE
          LLERAKEL.IDVIGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFNMYLL.IGGGFPGSEDVKLKFE
Retrocopy LLERAKELGIDVIGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFNMYLLEIGGGFPGSEDVKLKFE

Parental  EITSVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKLVLKEQTGSDDEEESTDRTFMYYVN
          EIT.VINPALDKYFPSDSG.RIIAEPGRYYVASAFTLAVNIIAKKLVLKEQTGSDDEEES...TFMYYVN
Retrocopy EITNVINPALDKYFPSDSGARIIAEPGRYYVASAFTLAVNIIAKKLVLKEQTGSDDEEESSEWTFMYYVN

Parental  DGVYGSFNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGAY
          DGVYGSFNCILYDHAHVKPLLQKRPK.DEKYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMG.Y
Retrocopy DGVYGSFNCILYDHAHVKPLLQKRPKSDEKYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGDY

Parental  TVAAASTFNGFQRPTIYYVMSGPTWQLMQQIRTQDF-PPGVEEPDVGPLPVSCAWESGMKR
          TV.AASTFNGFQRPTIYYVMSGPTWQLMQQIRTQ.F.PP.VEEPDVG.LP.SCA.ESG...
Retrocopy TVTAASTFNGFQRPTIYYVMSGPTWQLMQQIRTQEF<PPRVEEPDVGLLPMSCAQESGTRQ

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	12.11 RPM
ERP005899_muscle	0.05 RPM	172.20 RPM
SRP017611_brain	0.00 RPM	53.31 RPM
SRP017611_kidney	0.12 RPM	92.76 RPM
SRP017611_liver	0.00 RPM	33.98 RPM
SRP030211_testis	0.27 RPM	197.23 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_552 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552 ,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,