RetrogeneDB ID: retro_btau_1317

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:33507616..33508898(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000019276
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSBTAG00000014239
• Aliases: None
• Description: G2/mitotic-specific cyclin-B1 [Source:UniProtKB/Swiss-Prot;Acc:Q1LZG6]

Sequence

>retro_btau_1317
ATGGCGCTCCGGATCACCAGGAACACGAAGATTAATGCTGAAAATAAGGCGAAGATCAGTATGGCAGGGGCCAAGCGCGT
GCCTGTGGCCTCTGTTGCAACATCTAAGCCCGGGCTGAGGCCCCGAACAGCTCTTGGAGACATCGGTAACAAAGTCAGTG
AACAACCGCAGGCCAAACTGCCTCTGAAAAAGGAAGCAAAAACTTTAGCTGCTGGAAAAGTTACTGCTAAAAAAGTACCA
AAACCTCTGGAAAAGGCTCCTGTACCTGTGCCGGAGCCCCAGCCGGAGCCAGAGCCGGAACTCGAGCCTGTTAAGGAAGA
GAAACTTTCCCCGGAGCCTATTTTGGTCGATACTCCCCTCTCCAAGCCCCATGGAAACATCTGGCTGTGCCCCTGCAGAA
GAGTATCTGTGTCAGGCTTTCTCAGAGGTAATTCTTGCAGTGAGTGATGTGGATGCAGAAGACGGAGCGGATCCAAACCT
TTGTAGTGAATATGTAAAAGATATCTATGCTTATCTAAGACAACTTGAGGAAGAGCAAGCAGTCAAACCAAAATACCTAA
TGGGTCATGAAGTCACTGGAAACATGAGAGCCATCCTCATTGACTGGCTAGTGCAAGTTCAAATAAAATTCAGATTACTG
CAGGAGACCATGTACATGACTGTTTCCATAATTGATCGGTTCATGCAGGATAACTATGTGCCCAAGAAGATGCTGCAGCT
GGTTGGAGTCACTGCCATGTTTGCTGCAAGCAAATATGAGGAAATGTACCCTCCAGAAATCGGTGACTTTGCCTTTATGA
CTGACAACACCTACACCAAGTTTCAAATCAGACAGATGGAAATGAAGATTCTAAGAGCTTTAAGTTTTAGTCTGGGTCAC
CCTCTACCCCTGCATTTCCTTCGGAGAGCATCTAAGATTGGAGAGGTTGATGTTGAGCTACATACTCTGGCCAAATATTT
GATGGAACTAACTATGCTGGACTACGATATGGTGCACTTTCCTCCTTCTCAGATTGCAGTGGTAGCTTTTTGCTTAGCAC
TGAAAGTTCTTGATAATGGTGAATGGACACCAACTCTACAGCATTACCTGTCATATACTGAAGAATCCCTTCTTGTTGTT
ATGCAACACCTGGCAAAGAATGTGGTCATGGTGAACCGTGGGCTTACAAAGCACATGACTATCAAGAACAAGTATGCCAC
ATCTAAGCATGCTAAGATCAGCACTCTAGCACAGCTGAATTCTGCACTAGTTCAAGATTTAGCCAAGGCTGTGGCAAAGG
TG

Alignment

ORF - retro_btau_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALRITRNTKISAENKAKISMAGAKRVPVAAVATSKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTLA
          MALRITRNTKI.AENKAKISMAGAKRVPVA.VATSKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTLA
Retrocopy MALRITRNTKINAENKAKISMAGAKRVPVASVATSKPGLRPRTALGDIGNKVSEQPQAKLPLKKEAKTLA

Parental  SGKVTAKKVPKPLEKAPVPVPEPQPEPEPEPEHVKEDKLSPEPILVDTP-SPSPMETSGCAPAEEYLCQA
          .GKVTAKKVPKPLEKAPVP..............VKE.KLSPEPILVDTP.SPSPMETSGCAPAEEYLCQA
Retrocopy AGKVTAKKVPKPLEKAPVPXXXXXXXXXXXXXXVKEEKLSPEPILVDTP>SPSPMETSGCAPAEEYLCQA

Parental  FSDVILAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLMGREVTGNMRAILIDWLVQVQIK
          FS.VILAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLMG.EVTGNMRAILIDWLVQVQIK
Retrocopy FSEVILAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEEEQAVKPKYLMGHEVTGNMRAILIDWLVQVQIK

Parental  FRLLQETMYMTVSIIDRFMQDTYVPKKMLQLVGVTAMFVASKYEEMYPPEIGDFAFVTDNTYTKFQIRQM
          FRLLQETMYMTVSIIDRFMQD.YVPKKMLQLVGVTAMF.ASKYEEMYPPEIGDFAF.TDNTYTKFQIRQM
Retrocopy FRLLQETMYMTVSIIDRFMQDNYVPKKMLQLVGVTAMFAASKYEEMYPPEIGDFAFMTDNTYTKFQIRQM

Parental  EMKILRALNFSLGRPLPLHFLRRASKIGEVDVELHTLAKYLMELTMLDYDMVHFPPSQIAAGAFCLALKV
          EMKILRAL.FSLG.PLPLHFLRRASKIGEVDVELHTLAKYLMELTMLDYDMVHFPPSQIA..AFCLALKV
Retrocopy EMKILRALSFSLGHPLPLHFLRRASKIGEVDVELHTLAKYLMELTMLDYDMVHFPPSQIAVVAFCLALKV

Parental  LDNGEWTPTLQHYLSYTEESLLVVMQHLAKNVVMVNRGLTKHMTIKNKYATSKHAKISTLAQLNSALVQD
          LDNGEWTPTLQHYLSYTEESLLVVMQHLAKNVVMVNRGLTKHMTIKNKYATSKHAKISTLAQLNSALVQD
Retrocopy LDNGEWTPTLQHYLSYTEESLLVVMQHLAKNVVMVNRGLTKHMTIKNKYATSKHAKISTLAQLNSALVQD

Parental  LAKAVAKV
          LAKAVAKV
Retrocopy LAKAVAKV

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	0.50 RPM	1.30 RPM
ERP005899_muscle	0.00 RPM	13.67 RPM
SRP017611_brain	0.00 RPM	0.14 RPM
SRP017611_kidney	0.30 RPM	0.53 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	1.16 RPM	42.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1317 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004943	1 retrocopy	retro_btau_1335,
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317 , retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,