RetrogeneDB ID: retro_btau_6

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:19864722..19865715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000040418
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSBTAG00000011198
• Aliases: None
• Description: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P61287]

Sequence

>retro_btau_6
ATGTCCGACAGCGAGAAGCTCAACCTGGACTCCATCATCGGGCGCCTGCTGGAAGTGCAGGGCTCACGGCCTGGGAAGAA
CGTGCAGCTGACAGAGAACGAGATCCGTGGTCTGTGCCTCAAATCCCGGGAGATTTTCCTGAGCCAGCCCATTCTTCTGG
AGCTTGAGGCGCCCCTCAAGATCTGTGGTGACATCCATGGCCAGTACTATGACCTTCTACGGCTGTTTGAGTATGGTGGC
TTCCCTCCAGAGAGCAACTACCTCTTCTTGGGGGATTATGTAGATCGGGGCAAGCAGTCTTTGGAGACCATCTGCCTGTT
GCTGGCCTATAAGATCAGATACCCGGAGAATTTCTTTCTACTTCGTGGGAACCATGAGTGTGCCAGCATCAACCGCATTT
ATGGCTTCTATGATGAATGCAAGAGAAGATACAACATCAAACTGTGGAAGACGTTCACTGACTGCTTCAACTGCCTGCCC
ATTGCAGCCATTGTGGATGAGAAGATCTTTTGCTGCCACGGGGGCCTGTCTCCAGACTTGCAATCCATGGAGCAGATTAG
GCGTATTATGCGGCCCACAGACGTGCCTGACCAGGGCCTACTGTGTGATCTCCTGTGGTCTGACCCTGACAAGGATGTTC
AAGGCTGGGGCGAGAATGACCGTGGTGTCTCCTTTACCTTTGGGGCTGAGGTGGTAGCCAAGTTCCTGCACAAGCATGAT
TTGGACCTCATCTGCAGAGCACATCAGGTTGTAGAAGATGGCTATGAGTTCTTTGCCAAGAGACAGTTGGTGACACTCTT
CTCAGCTCCCAACTACTGTGGAGAGTTTGACAATGCTGGTGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCCTTCC
AGATCCTCAAGCCCGCTGATAAGAATAAGGGCAAGTATGGGCAGTTCAGCGGCCTGAACCCCGGAGGCCGGCCCATCACT
CCACCCCGCAATTCTGCCAAAGCCAAGAAATAG

Alignment

ORF - retro_btau_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 93.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          M.D..KLN.DSII.RLLEV.GS.PGKNVQL.ENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
Retrocopy MSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
          DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKI.YPENFFLLRGNHECASINRIYGFYDEC
Retrocopy DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIRYPENFFLLRGNHECASINRIYGFYDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
Retrocopy KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD

Parental  KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          KDV.GWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
Retrocopy KDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG

Parental  AMMSVDETLMCSFQILKPAEKKK
          AMMSVDETLMCSFQILKPA.K.K
Retrocopy AMMSVDETLMCSFQILKPADKNK

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	50.54 RPM
ERP005899_muscle	4.75 RPM	71.74 RPM
SRP017611_brain	0.82 RPM	57.74 RPM
SRP017611_kidney	2.96 RPM	60.16 RPM
SRP017611_liver	1.51 RPM	28.54 RPM
SRP030211_testis	0.76 RPM	339.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_6 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_6 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6 , retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,