RetrogeneDB ID: retro_btau_738

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:59365715..59366624(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047712
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSBTAG00000007160
• Aliases: None
• Description: Cyclin-dependent kinase 4 [Source:UniProtKB/Swiss-Prot;Acc:Q32KY4]

Sequence

>retro_btau_738
ATGGCTACCTCCTGATATGAGCCAGTGGCTGAGATTGGTGTCGGTGCCTATGGGACAGTGTACAAGGCCCGTGATCTCCA
CAGTGGCCACTTCATGGCCCTCAAGAGTGTAAGAGTCCCCAGTGGAGGTGGTGCTGGCGGGGGCCTGCCCATCAGCACCG
TTTGGGAGGTGGCCTTACTGCAGCGTCTGGAGGCTTTTGAGCATCCCAATGTTGTCAGGCTCATGGACGTCTGTGCAACG
GCCTGAACTGACCGGGAGACCAAAGTGACCCTGGTGTTTGAGCATGTGGACCAAGACCTAAGGACACATCTGGACAAGGG
ACCCCCACCAGACTTGCCAGTGGAGATCACAAAGGATCTGATGCACCAGTTTCCAAGAGGCCTGGATTTCCTTCATGCCA
ACTGCATCGTTCACCGAGACCTGAAGCCAGAGAACATTCTGGTGACAAATGGTGGGACAGTCAAGCTGGCTGCCTTTGGC
CTGGCCAGAATCCACAGCTACCAGATGGCACTTACACCTATGGTTGTTACAGTCTGGTATCGTGCTCCAGAAGTTCTTTT
GCAGTCTACATATGCAACACCCGTGGACATGTGGAGCGTTGGCTGTATCTTCGCAGAGATGTTTCGTCGAAAGCCTCTCT
TCTGTGGAAACTCTGAAGCTGACCAGTTAGGCAAAATCTTTGACCTGATCGGACTGCCCCCAGAGGATGACTGGACCCGA
GAGGTCTCTCTACCCCAAGGAGCCTTTTCCCCCAGAGGGCCCCGCCCAGTGCAGTCGGTGGTCCCTGAGCTGGAGGAATC
TGGAGCACAGCTGCTGCTGGAGATGCTGACTTTTAACCCACACAAGCGAATCTCTGCCTTCCAAGCCCTGCAGCAGTCTT
ATCTACACAAGGCAGAAGGTGACGCAGAG

Alignment

ORF - retro_btau_738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGAGGGLPISTVREVALLRRLEAFEHPN
          MATS.YEPVAEIGVGAYGTVYKARD.HSGHF.ALKSVRVP.GGGAGGGLPISTV.EVALL.RLEAFEHPN
Retrocopy MATS*YEPVAEIGVGAYGTVYKARDLHSGHFMALKSVRVPSGGGAGGGLPISTVWEVALLQRLEAFEHPN

Parental  VVRLMDVCATARTDRETKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCIVHRD
          VVRLMDVCATA.TDRETKVTLVFEHVDQDLRT.LDK.PPP.LPVE..KDLM.QF.RGLDFLHANCIVHRD
Retrocopy VVRLMDVCATA*TDRETKVTLVFEHVDQDLRTHLDKGPPPDLPVEITKDLMHQFPRGLDFLHANCIVHRD

Parental  LKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRR
          LKPENILVT.GGTVKLA.FGLARI.SYQMALTP.VVT.WYRAPEVLLQSTYATPVDMWSVGCIFAEMFRR
Retrocopy LKPENILVTNGGTVKLAAFGLARIHSYQMALTPMVVTVWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRR

Parental  KPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFSPRGPRPVQSVVPELEESGAQLLLEMLTFNP
          KPLFCGNSEADQLGKIFDLIGLPPEDDW.R.VSLP.GAFSPRGPRPVQSVVPELEESGAQLLLEMLTFNP
Retrocopy KPLFCGNSEADQLGKIFDLIGLPPEDDWTREVSLPQGAFSPRGPRPVQSVVPELEESGAQLLLEMLTFNP

Parental  HKRISAFRALQHSYLHKAEGDAE
          HKRISAF.ALQ.SYLHKAEGDAE
Retrocopy HKRISAFQALQQSYLHKAEGDAE

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	16.37 RPM
ERP005899_muscle	0.05 RPM	41.76 RPM
SRP017611_brain	0.05 RPM	11.56 RPM
SRP017611_kidney	0.00 RPM	36.87 RPM
SRP017611_liver	0.00 RPM	21.37 RPM
SRP030211_testis	0.04 RPM	16.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_738 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_738 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004021	1 retrocopy	retro_btau_1424,
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738 ,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Cavia porcellus	ENSCPOG00000002670	1 retrocopy	retro_cpor_457,
Dasypus novemcinctus	ENSDNOG00000014245	1 retrocopy	retro_dnov_145,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,