RetrogeneDB ID: retro_btau_1335

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:108156670..108157899(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046910
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.87491
• Ensembl ID: ENSBTAG00000004943
• Aliases: CCNA2, CCNA
• Description: Cyclin-A2 [Source:UniProtKB/Swiss-Prot;Acc:P30274]

Sequence

>retro_btau_1335
TTGCAGCAGACGGCGTTCCAGGAGGACAGGAGAACGTCAACCCCGAGAAGTAGGCGCCCACCCAGCAGCTCCGGACCCGG
GCTGGGCTGGCAGTACTGAGGGCCAGGAACTCGCGGGGTCCAGCTCCCCAGAGGCCTAAGACGTGACGGGTTGCACCTCT
TAAGGATCTTCCTATAAATGATGAGTATGTCCCTGTTCCTCCCTGGAAAGCAAACAATAAACAGCCTGCATTTACTATTC
ATGTGGATGAAGCAGAAGAAGAGGTTCAAAAGAGGCCAACTGAATCTAAAAAATCAGAAAGTGAAGATGTCTTGGCCTTT
AATTCAGCTGTTACTTTACCAGGACCAAGAAAGCCACTGGCACTTCTTGATTACCCAATGGATGGTAGTTTTGAGTCTCC
ACATACTATGGAAATGTCAGTTGTATTGGAAGATGAAAAGCCAGTGAGTGTTAATGAAGTACCAGACTACCATGAGGACA
TTCACACGTACCTTAGGGAAATGGAGGTTAAATGTAAGCCTAAAGTGGGTTACATGAAGGAACAGCCAGACATTACTAAC
AGTATGAGGGCTATCCTCGTGGACTGGTTAGTTGAAGTAGGAGAAGAATATAAACTGCAGAATAAGACCCTGCATTTGGC
TGTGAACTACATTGATAGGTTTCTTTCATGCATGTCTGTGTTGAGAGGAAAACTTCAACCTGTGGGCACTGCTGCTATGC
TTTTAGCCTCAAAGTTTGAAGAAATATACCCGCCAGAAGTAGCAGAGTTTGTATACAGTACAGATGACACTTATACCAAG
AAACAAGTTCTAAGGATGGAGCACCTAGTCTTGAAAGTCCTGGCTTTTGACTTAGCTGCACCAACAATAAATCAGTTTCT
TACCCAGTACTTTCTGCATCAGCAGCCGGCAAACTGCAAAGTTGAAAGTTTAGCAATGTTTTGGGGAGAGTTAAGTTTGA
TAGATGCTGACCCATATCTAAAGTATTTGCCGTCAGTTATCGCTGCAGCCTTTCATTTAGCACTCTACACAGTCACAGGA
CAAAGCTGGCCTGAATCATTAGTACAGAAGACTGGATATACTCTGAAAACTCTAAAGCCTTGTCTCCTGGACCTTCACCA
GACCTACCTCAGAGCACCACAGCACACATAACAGTCAATAAGAGAGAAGTACAAAAATTCAAAGTATCATGGTGTTTCTC
TCCTCAACCCACCAGAGACACTAAATGTG

Alignment

ORF - retro_btau_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.39 %
• Parental protein coverage: 95.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQQTAFQED-QENVNPEKAAPAQQPRTRAGLAVLRAGNSRGPAPQRPKTRRVAPLKDLPINDEYVPVPPW
          LQQTAFQED.QENVNPEK.AP.QQ.RTRAGLAVLRA.NSRGPAPQRPKT.RVAPLKDLPINDEYVPVPPW
Retrocopy LQQTAFQED<QENVNPEK*APTQQLRTRAGLAVLRARNSRGPAPQRPKT*RVAPLKDLPINDEYVPVPPW

Parental  KANNKQPAFTIHVDEAEE-IQKRPTESKKSESEDVLAFNSAVTLPGPRKPLAPLDYPMDGSFESPHTMEM
          KANNKQPAFTIHVDEAEE..QKRPTESKKSESEDVLAFNSAVTLPGPRKPLA.LDYPMDGSFESPHTMEM
Retrocopy KANNKQPAFTIHVDEAEEEVQKRPTESKKSESEDVLAFNSAVTLPGPRKPLALLDYPMDGSFESPHTMEM

Parental  SVVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNE
          SVVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMK.QPDITNSMRAILVDWLVEVGEEYKLQN.
Retrocopy SVVLEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKEQPDITNSMRAILVDWLVEVGEEYKLQNK

Parental  TLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLK
          TLHLAVNYIDRFLS.MSVLRGKLQ.VGTAAMLLASKFEEIYPPEVAEFVY.TDDTYTKKQVLRMEHLVLK
Retrocopy TLHLAVNYIDRFLSCMSVLRGKLQPVGTAAMLLASKFEEIYPPEVAEFVYSTDDTYTKKQVLRMEHLVLK

Parental  VLAFDLAAPTINQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAAAAFHLALYTVTGQ
          VLAFDLAAPTINQFLTQYFLHQQPANCKVESLAMF.GELSLIDADPYLKYLPSVI.AAAFHLALYTVTGQ
Retrocopy VLAFDLAAPTINQFLTQYFLHQQPANCKVESLAMFWGELSLIDADPYLKYLPSVI-AAAFHLALYTVTGQ

Parental  SWPESLVQKTGYTLETLKPCLLDLHQTYLRAPQHAQQSIREKYKNSKYHGVSLLNPPETLNV
          SWPESLVQKTGYTL.TLKPCLLDLHQTYLRAPQH..QSIREKYKNSKYHGVSLLNPPETLNV
Retrocopy SWPESLVQKTGYTLKTLKPCLLDLHQTYLRAPQHT*QSIREKYKNSKYHGVSLLNPPETLNV

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	2.38 RPM
ERP005899_muscle	0.37 RPM	12.72 RPM
SRP017611_brain	0.00 RPM	1.42 RPM
SRP017611_kidney	0.00 RPM	1.48 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.12 RPM	13.99 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1335 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1335 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 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,
Macropus eugenii	ENSMEUG00000000128	1 retrocopy	retro_meug_32,
Myotis lucifugus	ENSMLUG00000005161	1 retrocopy	retro_mluc_400,
Monodelphis domestica	ENSMODG00000018931	1 retrocopy	retro_mdom_1309,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169,