RetrogeneDB ID: retro_btau_1523

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:14289972..14290719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSBTAG00000021045
• Aliases: None
• Description: transcription factor E2F3 [Source:RefSeq peptide;Acc:NP_001179767]

Sequence

>retro_btau_1523
AAGTAAAGGATTTATGACATCAACAAAGTCCTGGAAGGCATCCACCTCATTAAGAAGTCTGAAAACGACGTGCAGTGGAT
GGGCTGCAGTCTATCTGAGGACAGGGCCACACTGGCCTAGTGTCAAGGCCTGTCAAAAGTGACCGAGCTCAGTCAGGAAG
AGAAGAAATTAGATGAACTGATCCAAAGCTGCACCCTGGACCTCAAACTGCTAACGGAGGATTCAGAGAATCAAAGGTTA
GCTTATGTTACATATCAGGATATTTGAAAAATTAGTGGCCTTAAAGACCAAACTGTTAATAGTTGTGAAAGCCCCTCCAG
AAACATGACTTGAAGCGCCTGACCCAATAGAGAGCCTATAAATACATTTGGCAAGTACCCAAGGACCCATTGAGGTTTAT
TTGTGTCCAGAAGAGTCTGAAACACACAGTCCAATGAAAGCAAACAGCCAGGCCACAAAGGGAATATCCCTAAGCCCACT
TCCAAAGACTTGGCTTCAACCAACTCAGGACATAGTGATTGCTTGATTTCTATGACAAACCTTTTCTCCTCTGGCCTCCC
TCGCCAACCTTTTACAGCAGACTGAGGACCCAATTCCTTCCAATCTAGAAGGACCATTTGTGAACTTACTGCCTCCCTTG
CTCCAAGAGGACTATCTCCTAAACCTCAAGGAGGAAGAAAGCATCAATGATCTCTTTGATGCTTACGATTTGAAAAGCGT
CTGCTGGTGGAAGACTTTATGTGTAGT

Alignment

ORF - retro_btau_1523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 54.21 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDL
          K.RIYDI..VLEGIHLIKK.S.N.VQWMGCSLSED...LA.CQGLSK.VTELSQEEKKLDELIQSCTLDL
Retrocopy K*RIYDINKVLEGIHLIKK-SENDVQWMGCSLSEDRATLA*CQGLSK-VTELSQEEKKLDELIQSCTLDL

Parental  KLLTEDSENQRLAYVTYQDIRKISGLKDQTV-IVVKAPPETRLEVPDPIESLQIHLASTQGPIEVYLCPE
          KLLTEDSENQRLAYVTYQDI.KISGLKDQTV.IVVKAPPET.LE.PDPIESL.IHLASTQGPIEVYLCPE
Retrocopy KLLTEDSENQRLAYVTYQDI*KISGLKDQTV>IVVKAPPET*LEAPDPIESL*IHLASTQGPIEVYLCPE

Parental  ETETHSPMKTNNQ-DHNGNIPKPTSKDLASTNSGHSDCSISMANL-SPLASPANLLQQTEDQIPSNLEGP
          E.ETHSPMK.N.Q..H.GNIPKPTSKDLASTNSGHSDC.ISM.NL.SPLAS.ANLLQQTED.IPSNLEGP
Retrocopy ESETHSPMKANSQ<GHKGNIPKPTSKDLASTNSGHSDCLISMTNL>SPLASLANLLQQTEDPIPSNLEGP

Parental  FVNLLPPLLQEDYLLSLGEEEGISDLFDAYDL-EKLPLVEDFMCS
          FVNLLPPLLQEDYLL.L.EEE.I.DLFDAYDL.EK..LVEDFMCS
Retrocopy FVNLLPPLLQEDYLLNLKEEESINDLFDAYDL<EKRLLVEDFMCS

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	0.07 RPM	0.94 RPM
ERP005899_muscle	0.00 RPM	1.74 RPM
SRP017611_brain	0.00 RPM	2.60 RPM
SRP017611_kidney	0.00 RPM	3.97 RPM
SRP017611_liver	0.00 RPM	1.59 RPM
SRP030211_testis	0.08 RPM	7.14 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1523 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1523 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009378	1 retrocopy	retro_btau_1002,
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523 ,
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796, retro_ggor_2254,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,