RetrogeneDB ID: retro_btau_1159

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:25355297..25356546(-)
• Located in intron of: ENSBTAG00000033413

Retrocopy information

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

Parental gene information

• Parental gene symbol: METT10D
• Ensembl ID: ENSBTAG00000017440
• Aliases: METTL16, METT10D
• Description: methyltransferase-like protein 16 [Source:RefSeq peptide;Acc:NP_001179145]

Sequence

>retro_btau_1159
AGCCACTTATCTGATCTTATAAAAGTAGTTAAAGTACTACAGAAGACACTCCTGATGGATGCTCTTAAAGAAGAATCTGA
GATACTTATGACTTTTGCATGTGCAACCCTGCCTTTTTTGCCAATCAGTTGGAAGCCAAGGGAGTGAATTCTGAGTGAAT
TCTCGAAATCCTTGAAGACCCCTACCCAGTTCTGTAAATACAGGAGGAAGCACAAAGATCATGGCAGAAGGAGGTAAATT
AGAGTTTGTTAAAAGGATCATCCACAACAGTTTACAGCTTAAAAAAAGATTAAGATGGTATAGCCGTATGCTAGGGAAAA
AAATGCAGCCTGGCTCCTCTGAAGGAAGAACTTCGCATACAAGGGGTTCCTAAAGTCACCTATACTGAATTCTGCCAGGG
TCAGACAATGAGATGGGCTTTGGCTTGGAGTTTTTATGATGACTAACAGTACCATTACCACCCAGTAAGCAAAGAAAACT
AGAGAAGCCAAGGAAGCCCATTACGTTTGTAGTCCTCGGGCCTGTGATGAAAGAACTAGCCCTCAAAGCGCCATCTCTGG
GCCCTGAGACAGTGGAAGGCATCGTGGTTGTGACAACATGGGTTGAAAAAATCCTCACTCATCTAAAGGTCCAGCATAAA
TGAGTTCCCTGTGGAAAGGAGGAAATCAGCCTTTTCCTAACAGCCCTAGAAAACTCCTGGATTCACTTAAGGAGGAAGAA
AAGAGACCGAGTGAGACAACTGAGAGAAGTGCCCCTAGCTCCCAAGAACGTGATCGAAGCCTTGGAAGAGAAAAAGTCTG
CCCCCAAAGAGTCTGGCAGTAGTCAGGATGTTGCCCAGGCCCCCCAGGAGAGTGCCCTGGGGGGTCCTGCTCCACCGGAA
GGCGAGTCTGCCACTGTGGGGGGCCACGGCCCCAGCCAGGACTCGCTTTCCCAGGAGGAAAACCCAGAACCCACAGAGGA
TGAAAGGAGTGAGGAAAAGGGGGGCATGGAGGTTCTGGAAGGTTGTAAAGGCTCTAGTAATGGAGCCCAGGACCACGAGG
CTCCTGAGCCCTTCAGCAGCCCAGTGTCTGAAAAAGGGAACCATCTCCAAGGAGTGGCTGGACGTTACTTATTCAAGTGT
CTGATAAACGTTAAGAAGGAGGTAGATGACGCCTTAGTTGAAATGCACTGGGTTGAGGGCCAGAACAGGGATTTGATGAC
CCAGCTTTGTACTTATATACATAACCAAATTTTCAGGCTTGTTGCTAGT

Alignment

ORF - retro_btau_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 73.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NNLSDLIKVVKVPQKTLLMDALKEESEII-YDFCMCN-PPFFANQLEAKG----VNSRNPRRPPPSSVNT
          ..LSDLIKVVKV.QKTLLMDALKEESEI..YDFCMCN.P..F.......G....VNSRNP.RP.PSSVNT
Retrocopy SHLSDLIKVVKVLQKTLLMDALKEESEIL<YDFCMCN<PCLFCQSVGSQGSEF*VNSRNP*RPLPSSVNT

Parental  GGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKK-CSLAPLKEELRIQGVPKVTYTEFCQGRTM
          GG.T.IMAEGG.LEFVKRIIH.SLQLKKRLRWYS.MLGKK.CSLAPLKEELRIQGVPKVTYTEFCQG.TM
Retrocopy GGSTKIMAEGGKLEFVKRIIHNSLQLKKRLRWYSRMLGKK>CSLAPLKEELRIQGVPKVTYTEFCQGQTM

Parental  RWALAWSFYDD-VTVPSPPSKRRKLEKPRKPITFVVLGPVMKELALKASSLGPETVEGIVVVTTWIEKIL
          RWALAWSFYDD..TVP.PPSK.RKLEKPRKPITFVVLGPVMKELALKA.SLGPETVEGIVVVTTW.EKIL
Retrocopy RWALAWSFYDD<LTVPLPPSKQRKLEKPRKPITFVVLGPVMKELALKAPSLGPETVEGIVVVTTWVEKIL

Parental  TDLKVQHKRVPCGKEEISLFLTAIENSWIHLRRKKRDRVRQLREVPLAPKDVIEALEEKKPPPRESGSSQ
          T.LKVQHK.VPCGKEEISLFLTA.ENSWIHLRRKKRDRVRQLREVPLAPK.VIEALEEKK..P.ESGSSQ
Retrocopy THLKVQHK*VPCGKEEISLFLTALENSWIHLRRKKRDRVRQLREVPLAPKNVIEALEEKKSAPKESGSSQ

Parental  DVAQGPQESALGGPAPPEGESATVGGHGPSQDLLSQEENPEPTEDERSEEKGDMEVLEGCKGSSNGAQDH
          DVAQ.PQESALGGPAPPEGESATVGGHGPSQD.LSQEENPEPTEDERSEEKG.MEVLEGCKGSSNGAQDH
Retrocopy DVAQAPQESALGGPAPPEGESATVGGHGPSQDSLSQEENPEPTEDERSEEKGGMEVLEGCKGSSNGAQDH

Parental  EAPEPFSSPASEKGNHLQGVAGRYLFKCLINVKKEVDDALVEMHWVEGQNRDLMNQLCTYIRNQIFRLVA
          EAPEPFSSP.SEKGNHLQGVAGRYLFKCLINVKKEVDDALVEMHWVEGQNRDLM.QLCTYI.NQIFRLVA
Retrocopy EAPEPFSSPVSEKGNHLQGVAGRYLFKCLINVKKEVDDALVEMHWVEGQNRDLMTQLCTYIHNQIFRLVA

Parental  S
          S
Retrocopy S

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	0.14 RPM	3.53 RPM
ERP005899_muscle	0.26 RPM	13.62 RPM
SRP017611_brain	0.05 RPM	10.73 RPM
SRP017611_kidney	0.12 RPM	10.43 RPM
SRP017611_liver	0.00 RPM	4.00 RPM
SRP030211_testis	0.28 RPM	11.00 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1159 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1159 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017440	2 retrocopies	retro_btau_1159 , retro_btau_1533,
Myotis lucifugus	ENSMLUG00000003531	2 retrocopies	retro_mluc_1130, retro_mluc_1625,
Monodelphis domestica	ENSMODG00000010765	2 retrocopies	retro_mdom_305, retro_mdom_339,
Otolemur garnettii	ENSOGAG00000004504	1 retrocopy	retro_ogar_491,
Ictidomys tridecemlineatus	ENSSTOG00000011876	1 retrocopy	retro_itri_1568,