RetrogeneDB ID: retro_btau_1266

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:29638729..29639508(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15H11orf46
• Ensembl ID: ENSBTAG00000012417
• Aliases: ARL14EP, ARF7EP, C11orf46, C15H11orf46
• Description: ARF7 effector protein [Source:UniProtKB/Swiss-Prot;Acc:Q5EA92]

Sequence

>retro_btau_1266
ATGATGGATCCATGTTCAGTTGGAGTCCAGCTTTGGACCACAAATGAGTGCCATAAAACCCATTATACTCGTCATAAGGT
TTCAAGACTTTGCAAGAATTGTCATCAAATGACATGCTTCTACTTCAACTGAGAACTGGAATGACACTTTCTGGGAACAA
TACAATTTGCTTCCATCATGCAAAAGTTTACATGGACAGATTTGATGATTTGCAGAAGTCATGTTGTGACCCATTTAACA
TACACAAAAAACTAGCCAAAAAAAATTTACATGTAATTGATTTAGATGATGCCACTTTTCTGAGTGCAAAATTTGGAAGA
CAGCTTGTACCTGGTTAGAAACTTTGTCCAAAATGTACACAGATAATCAATGGAAGTGTGGATGTTGATTCTGAAGACCG
GCAGAAAAGAAAACCTGACTCAGATGGAAGAACTGCTAAAGCTTTGAGGTCATTACAATTTGCAAACCCAGGAAAACAAA
CTGAATTTGCTCCAGAAACTGGTAAAAGAGAAAAAAGAAGGCTTACCAAAAATGCAACAGCTGGTTCAGACAGACAAGTG
ATCCTGGCAAAGAGTAAGATCTACAATAGCCAGGGTCTCCGGATTTTCAGCGGAATGGACCTCTGTCACTGCCTCGATGA
AGACTGCTTAGGCTGTTTCTATGCTTGTCCTGCCTGCGGTTCTACCAAATGTGGTACCGAATGCTGCTGTGATCAAAAGT
GGCTGTATGAGCAAACTGAAATCGAAGGAGGAGAAATAATTCATAACAAACATGCTGGA

Alignment

ORF - retro_btau_1266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMDPCSVGVQLRTTNECHKTYYTRHT-GFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKVYIDRFE
          MMDPCSVGVQL.TTNECHKT.YTRH..GFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKVY.DRF.
Retrocopy MMDPCSVGVQLWTTNECHKTHYTRHK<GFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKVYMDRFD

Parental  DLQKSCCDPFNIHKKLAKKNLHVIDLDDATFLSAKFGRQLVPGWKLCPKCTQIINGSVDVDSEDRQKRKP
          DLQKSCCDPFNIH.......LHVIDLDDATFLSAKFGRQLVPG.KLCPKCTQIINGSVDVDSEDRQKRKP
Retrocopy DLQKSCCDPFNIHXXXXXXXLHVIDLDDATFLSAKFGRQLVPG*KLCPKCTQIINGSVDVDSEDRQKRKP

Parental  DSDGRTAKALRSLQFANPGKQTEFAPETGKREKRRLTKNATAGSDRQVIPAKSKVYDSQGLLIFSGMDLC
          DSDGRTAKALRSLQFANPGKQTEFAPETGKREKRRLTKNATAGSDRQVI.AKSK.Y.SQGL.IFSGMDLC
Retrocopy DSDGRTAKALRSLQFANPGKQTEFAPETGKREKRRLTKNATAGSDRQVILAKSKIYNSQGLRIFSGMDLC

Parental  DCLDEDCLGCFYACPACGSTKCGAECRCDRKWLYEQIEIEGGEIIHNKHAG
          .CLDEDCLGCFYACPACGSTKCG.EC.CD.KWLYEQ.EIEGGEIIHNKHAG
Retrocopy HCLDEDCLGCFYACPACGSTKCGTECCCDQKWLYEQTEIEGGEIIHNKHAG

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	13.19 RPM
ERP005899_muscle	0.11 RPM	22.22 RPM
SRP017611_brain	0.18 RPM	18.04 RPM
SRP017611_kidney	0.06 RPM	18.37 RPM
SRP017611_liver	0.08 RPM	8.53 RPM
SRP030211_testis	0.29 RPM	103.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1266 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1266 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012417	1 retrocopy	retro_btau_1266 ,
Choloepus hoffmanni	ENSCHOG00000012698	1 retrocopy	retro_chof_1155,
Felis catus	ENSFCAG00000028620	1 retrocopy	retro_fcat_437,
Microcebus murinus	ENSMICG00000011547	2 retrocopies	retro_mmur_1003, retro_mmur_131,
Macaca mulatta	ENSMMUG00000017590	2 retrocopies	retro_mmul_1793, retro_mmul_984,
Mus musculus	ENSMUSG00000027122	1 retrocopy	retro_mmus_3319,