RetrogeneDB ID: retro_btau_42

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:13902928..13904173(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000008853
• Aliases: HNRNPF, HNRPF
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000020513
• Aliases: None
• Description: None

Sequence

>retro_btau_42
ATGATGTTGGGCCCTGAGGGAGGTGAAGGCTTTGTGGTCAAGCTCCGTGGCCTGCCCTGGTCCTGCTCTGTTGAGGATGT
GCAGAATTTCCTCTCCGACTGCACGATCCATGACGGGGTCGCAGGTGTTCACTTTATCTACACTAGAGAAGGCAGGCAGA
GTGGTGAGGCTTTTGTCGAACTTGAATCAGAAGATGACGTAAAATTGGCCCTTAAAAAAGACAGGGAAAGCATGGGACAT
CGGTACATTGAAGTGTTCAAGTCCCACAGAACCGAGATGGATTGGGTGTTGAAGCACAGTGGTCCAAACAGTGCTGACAC
TGCCAATGATGGTTTCGTGCGACTTCGAGGACTCCCGTTTGGATGCACCAAGGAAGAGATCATTCAGTTTTTCTCAGGGT
TGGAAATCGTGCCAAACGGGATCACATTGCCTGTGGACCCCGAGGGCAAGATTACAGGGGAAGCCTTTGTGCAGTTTGCC
TCACAGGAGTTAGCAGAGAAGGCTCTAGGGAAGCACAAGGAGAGAATAGGGCACAGGTATATTGAGGTGTTCAAGAGCAG
TCAGGAAGAAGTTAGGTCATACTCGGATCCCCCACTGAAGTTCATGTCAGTGCAGCGGCCAGGGCCCTATGACCGCCCTG
GCACAGCCAGGAGGTATATTGGCATCGTCAAGCAGGCAGGTCTGGAGAGGATGAGGTCTGGTGCCTACAGTGCAGGCTAT
GGGGGGTATGAGGAGTACAGCGGCCTCAGTGATGGCTACGGCTTCACCACCGACCTGTTTGGGAGAGACCTCAGTTACTG
TCTCTCTGGAATGTACGACCACAGGTATGGAGATGGTGAGTTCACTGTCCAGAGCACCACTGGACACTGTGTCCACATGA
GAGGTCTGCCCTACAAAGCCACAGAGAACGACATTTACAACTTCTTCTCCCCGCTCAACCCTGTGAGAGTCCACATTGAG
ATCGGCCCTGATGGAAGAGTGACCGGCGAAGCTGATGTTGAGTTTGCCACTCATGAAGAAGCCGTGGCGGCCATGTCCAA
AGACAGGGCCAATATGCAACATCGATACATAGAACTTTTCTTAAATTCCACAACAGGGGCCAGCAACGGGGCATATAGCA
GCCAGATGATGCAAGGCATGGGGGTGTCAACCCAGTCCACTTACAGTGGCCTTGAGAGCCAGTCTGTGAGCGGCTGTTAC
GGGGCTGGCTATGGTGGCCAGAACAGCATGGGTGGATATGACTAG

Alignment

ORF - retro_btau_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMLGPERDEGFLVKLHGLPWSCSVKDVQNFLSNCMIRDGVTCVHFIYSTEGRQSGELHQLFLELQS-DDV
          MMLGPE..EGF.VKL.GLPWSCSV.DVQNFLS.C.I.DGV..VHFIY..EGRQSGE....F.EL.S.DDV
Retrocopy MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEA---FVELESEDDV

Parental  KMALKKDRVSMGHWYIEVFKSHRTEMELVLKHSGPNSGDSSSDGFVRLRGLPFGCT-EDIIQFFSGLEIM
          K.ALKKDR.SMGH.YIEVFKSHRTEM..VLKHSGPNS.D...DGFVRLRGLPFGCT.E.IIQFFSGLEI.
Retrocopy KLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADTANDGFVRLRGLPFGCTKEEIIQFFSGLEIV

Parental  PNRITLPVDPEGKTTGEAFVQFASQELAEKALGKNKKRIIGHRYIEVFNSSQEGVRSYLDPPLKFMSVQL
          PN.ITLPVDPEGK.TGEAFVQFASQELAEKALGK.K.RI.GHRYIEVF.SSQE.VRSY.DPPLKFMSVQ.
Retrocopy PNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERI-GHRYIEVFKSSQEEVRSYSDPPLKFMSVQR

Parental  PGPYDRPGTARRYTGIIKQAGLERMRSGAYSAGYGGHEEYSSLGDGYGFTTDLFGRDLSYCLSEIYDHRY
          PGPYDRPGTARRY.GI.KQAGLERMRSGAYSAGYGG.EEYS.L.DGYGFTTDLFGRDLSYCLS..YDHRY
Retrocopy PGPYDRPGTARRYIGIVKQAGLERMRSGAYSAGYGGYEEYSGLSDGYGFTTDLFGRDLSYCLSGMYDHRY

Parental  RDGEFTVQSTTGHCVHMRGLPYKATENDIYNF-SLLNPVRVHIEIGPDGRVTSEADVEFATHEEAMVAMS
          .DGEFTVQSTTGHCVHMRGLPYKATENDIYNF.S.LNPVRVHIEIGPDGRVT.EADVEFATHEEA..AMS
Retrocopy GDGEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS

Parental  KNRANMQHRYIELFLNSTTGASNGSYSSQMMQDMGVSTQSTYSGLESQSVSGRYGAGYGAQNSMGRYD
          K.RANMQHRYIELFLNSTTGASNG.YSSQMMQ.MGVSTQSTYSGLESQSVSG.YGAGYG.QNSMG.YD
Retrocopy KDRANMQHRYIELFLNSTTGASNGAYSSQMMQGMGVSTQSTYSGLESQSVSGCYGAGYGGQNSMGGYD

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	142.39 RPM	0.00 RPM
ERP005899_muscle	160.53 RPM	0.00 RPM
SRP017611_brain	79.30 RPM	0.00 RPM
SRP017611_kidney	194.83 RPM	0.24 RPM
SRP017611_liver	198.66 RPM	0.00 RPM
SRP030211_testis	300.14 RPM	0.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_42 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_42 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_42 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Bos taurus	ENSBTAG00000020513	1 retrocopy	retro_btau_42 ,
Bos taurus	ENSBTAG00000021838	1 retrocopy	retro_btau_847,
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,