RetrogeneDB ID: retro_btau_640

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:19672677..19673180(-)
• Located in intron of: ENSBTAG00000006188

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSBTAG00000031069
• Aliases: None
• Description: Sorting nexin-24 [Source:UniProtKB/Swiss-Prot;Acc:Q17QS1]

Sequence

>retro_btau_640
ATGAAGGTCTACATCCTGTCCTTTTGCTACGAGGAGAGTGACCTGGAGCAGGGATACACGGTGTTTAAGATAGAAGTGCT
AATGAATGGAAGAAAACATTTTGTTGAAAAAAGGTACAGCGAATTACATGCCCTGCACAAAAAGCTTAAGAAAGATATTA
AAACCCCAGAAATTCCTTCTAAACATGTTTGGAACTGGATCCCAAATGTTGGAACAGCGATGACAAGGTTTGAAACCTAT
TTACAGGCTGTCATTCTGGAAAATGAAGAACTTCCCAAACTATTTCTTGATTTCCTAAATGTTCAACATTTGCCCTCTCT
ACCAAAGACAGAGTTTTGTGGATCTTTTGATGAGACAGAGTCTGAAGAGTAAAGCAAACTGTTCCACCAGCCGGTGCTGC
TGTTCTCAGGGATCCATACGTCTTGCTTACAGCCAGTGATTTTCCAAATGTGGTTACTGAAGAAGTTCTCCATGGGATAT
TTTACCCTCATCTACAACCCAGG

Alignment

ORF - retro_btau_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKV
          M.VYI.SF.YEESDLE.GYTVFKIEVLMNGRKHFVEKRYSE.HALHKKLKK.IKTPEIPSKHV.NW.P.V
Retrocopy MKVYILSFCYEESDLEQGYTVFKIEVLMNGRKHFVEKRYSELHALHKKLKKDIKTPEIPSKHVWNWIPNV

Parental  LEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKTESYGSFDETESEESSKLSHQPVLLF-LRD
          ........ETYLQAVILENEELPKLFLDFLNV.HLPSLPKTE..GSFDETESEE.SKL.HQPVLLF.LRD
Retrocopy GTAMTR-FETYLQAVILENEELPKLFLDFLNVQHLPSLPKTEFCGSFDETESEE*SKLFHQPVLLF<LRD

Parental  PYVLPAASDFPNVVIEGVLHGIFYPHLQPR
          PYVL..ASDFPNVV.E.VLHGIFYPHLQPR
Retrocopy PYVLLTASDFPNVVTEEVLHGIFYPHLQPR

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	44.34 RPM
ERP005899_muscle	0.00 RPM	18.27 RPM
SRP017611_brain	0.00 RPM	14.34 RPM
SRP017611_kidney	0.00 RPM	30.58 RPM
SRP017611_liver	0.00 RPM	10.19 RPM
SRP030211_testis	0.01 RPM	3.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_640 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031069	1 retrocopy	retro_btau_640 ,
Choloepus hoffmanni	ENSCHOG00000006859	2 retrocopies	retro_chof_1841, retro_chof_544,
Dasypus novemcinctus	ENSDNOG00000019810	1 retrocopy	retro_dnov_261,
Echinops telfairi	ENSETEG00000010310	1 retrocopy	retro_etel_923,
Microcebus murinus	ENSMICG00000001708	1 retrocopy	retro_mmur_1043,
Myotis lucifugus	ENSMLUG00000009392	2 retrocopies	retro_mluc_1022, retro_mluc_2330,
Monodelphis domestica	ENSMODG00000013427	1 retrocopy	retro_mdom_1215,
Otolemur garnettii	ENSOGAG00000005170	2 retrocopies	retro_ogar_2940, retro_ogar_975,
Sorex araneus	ENSSARG00000009785	1 retrocopy	retro_sara_99,
Sarcophilus harrisii	ENSSHAG00000011329	1 retrocopy	retro_shar_488,
Tarsius syrichta	ENSTSYG00000014395	2 retrocopies	retro_tsyr_1563, retro_tsyr_1691,