RetrogeneDB ID: retro_btau_1412

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:25868504..25869206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.87402
• Ensembl ID: ENSBTAG00000018382
• Aliases: None
• Description: Spermine synthase [Source:UniProtKB/Swiss-Prot;Acc:Q3SZA5]

Sequence

>retro_btau_1412
GCTGATGGTGAGACCATTCTGAAAGGCCTCCAGTCCATTTTCCAGGAGCAGGGGATGACGAAGTCAGTGCACACCTGGCA
GGACCATGGCTATTTAGCGACGTACATAAACAAAAACGGCAGCTTTGCCAATTTGAGAATCTACCCGCATGGATTGGTGT
TGCTGGATCTTCAGAGCTACGACGGCGACGCACAAGGCAAAGAAGTCGATAGTCTTTTGAACAAAGTAGAAGAAAGAATG
AAAGAATTGAGTCAGGACAGTACTGAGCGGGTAAAGCGATTACCACCCATAGTTCGAGGAGGGGCCATTGACAGATACTG
GCCCACTGCGGATGGTCGCCTGGTTGAGTACGACATAGATAAAGTGGTGTATGACGAAGACTCACCTTACCAGAACATTA
AAATTTTACTCTCAAAGCAATTTGGGAATATTATCATCCTCAGTGGGGATGTTAATTTGGTGGAAAGTGATTTGGCGTAT
ACCCGGGCCATCATGGGCAGTGGCAAAGAAGATTACAGTGGCAAAGATGTACTAATTCTGGGAGGTGGAGATGGGGGCAT
ATTATGTGAAATAGTCAAACTGAAACCAAAGATGGTGACTATGGTAGAGATTGACCAAATGGTGATTGACGGATGTAAGA
AATACATGTGAAAAACGTGTGGTGATGTCTTAGACAATCTTAAAGGAGACTGCTATCAGGTT

Alignment

ORF - retro_btau_1412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 67.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADGETILKGLQSIFQEQGMTESVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVD
          ADGETILKGLQSIFQEQGMT.SVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVD
Retrocopy ADGETILKGLQSIFQEQGMTKSVHTWQDHGYLATYINKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEVD

Parental  SLLNKVEERMKELSQDSTERVKRLPPIVRGGAIDRYWPTADGRLVEYDIDKVVYDEDSPYQNIKILHSKQ
          SLLNKVEERMKELSQDSTERVKRLPPIVRGGAIDRYWPTADGRLVEYDIDKVVYDEDSPYQNIKIL.SKQ
Retrocopy SLLNKVEERMKELSQDSTERVKRLPPIVRGGAIDRYWPTADGRLVEYDIDKVVYDEDSPYQNIKILLSKQ

Parental  FGNILILSGDVNLAESDLAYTRAIMGSGKEDYSGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVID
          FGNI.ILSGDVNL.ESDLAYTRAIMGSGKEDYSGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVID
Retrocopy FGNIIILSGDVNLVESDLAYTRAIMGSGKEDYSGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVID

Parental  GCKKYMRKTCGDVLDNLKGDCYQV
          GCKKYM.KTCGDVLDNLKGDCYQV
Retrocopy GCKKYM*KTCGDVLDNLKGDCYQV

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	0.22 RPM	39.80 RPM
ERP005899_muscle	7.81 RPM	74.59 RPM
SRP017611_brain	2.70 RPM	17.54 RPM
SRP017611_kidney	7.23 RPM	66.98 RPM
SRP017611_liver	3.62 RPM	24.62 RPM
SRP030211_testis	0.49 RPM	3.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1412 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1412 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412 ,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,