RetrogeneDB ID: retro_btau_1753

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:85743538..85744283(+)
• Located in intron of: ENSBTAG00000012543

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSBTAG00000034495
• Aliases: None
• Description: General transcription factor IIF subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q2T9L9]

Sequence

>retro_btau_1753
ATGGCTGAAAGCAGGGAACTTGACGTGACAGGCGCCAAACAGAACACCAGAATGTGGCGGGTCAGGGTTCTTTGATATCT
GTCACTGCAATGGGCTAAGGCCCCTGAAAGAAGTGAAGTTGGAAAACTGTGGATTTCCAAAAATCAAGGAAGGACCAAGG
TGTTATTTACTTTGAAAGAGGATCTTGCAAATACTTATGATATTGGCAGAAAAATAGCTTCAGTCAGTGCTCTAGAGAAC
ATGAATTTATCTTGCAAAGTGTTAGAGGACAGACATTAACAGGGTTTACTCAGAGCTCATCAGATAAGCTTTCACTGGAA
GGAATAGTGGTACAAAGAGCTGAATGCTGACCCGCTGCCAGTGAAAACTACCAGCGATTCAAGAGATTACAAATAGAAGA
ATCTTCCAATTCTGTAAGGCTACCACAGCACCTGGACAAAGTTGTGACAACCAATTACAAACCTGTTGCTAATCATCAAT
ACAATATAGAATATAAAAGGAAAAAGAAGAAGATGGAAAACAAGTTTGAACTGATAAACAACACATTTTAGACAAGCTGG
TTTTGGCTTTTGAGAAACATCAATATTATAATCTTAAGGACTTGGAGGACACCACAAAACAGCCTGTGTTGTACCTGAAG
GAAATCTTAAAAGAAATTGGTATTCAAGATGTAAAAGGGATCCACAAAGACACATGGGAACTGAAACCAGAGTACAGACA
TTCTCAAGGAGAAGAAAAGAGTGAT

Alignment

ORF - retro_btau_1753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAERGELDLTGAKQNTGVWLVKVPKYLSQQWAKAPGRGEVGKLRIAKNQGRTEVSFTLNEDLANIHDIGG
          MAE..ELD.TGAKQNT..W.V.V..YLS.QWAKAP.R.EVGKL.I.KNQGRT.V.FTL.EDLAN..DIG.
Retrocopy MAESRELDVTGAKQNTRMWRVRVL*YLSLQWAKAPERSEVGKLWISKNQGRTKVLFTLKEDLANTYDIGR

Parental  KPASVSA-PREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAANENYMRLKRLQIEESSKPV
          K.ASVSA..REH.F.LQSV.GQTLT.FT.SSSDKLSLEGIVVQRAEC.PAA.ENY.R.KRLQIEESS..V
Retrocopy KIASVSA<SREHEFILQSVRGQTLTGFTQSSSDKLSLEGIVVQRAEC*PAASENYQRFKRLQIEESSNSV

Parental  RLSQQLDKVVTTNYKPVANHQYNIEYERKKK-EDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQ
          RL.Q.LDKVVTTNYKPVANHQYNIEY.RKKK.EDGK....DKQH.LD.L..AFEKHQYYNLKDL.D.TKQ
Retrocopy RLPQHLDKVVTTNYKPVANHQYNIEYKRKKK<EDGKQV*TDKQHILDKLVLAFEKHQYYNLKDLEDTTKQ

Parental  PVSYLKDILKEIGVQNVKGIHKNTWELKPEYRHYQVEEKSD
          PV.YLK.ILKEIG.Q.VKGIHK.TWELKPEYRH.Q.EEKSD
Retrocopy PVLYLKEILKEIGIQDVKGIHKDTWELKPEYRHSQGEEKSD

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	6.27 RPM
ERP005899_muscle	0.00 RPM	8.50 RPM
SRP017611_brain	0.00 RPM	6.21 RPM
SRP017611_kidney	0.00 RPM	7.88 RPM
SRP017611_liver	0.00 RPM	4.83 RPM
SRP030211_testis	0.00 RPM	22.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1753 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1753 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753 , retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850,