RetrogeneDB ID: retro_btau_1471

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:104332737..104333628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC37A3
• Ensembl ID: ENSBTAG00000012239
• Aliases: None
• Description: Sugar phosphate exchanger 3 [Source:UniProtKB/Swiss-Prot;Acc:Q17QZ3]

Sequence

>retro_btau_1471
GCCTGGCCAAGTATTTTTCAGAGAGGAACTGTGCTCTCCCAGTTCAGCCATCACCACGTGGTCACATCCCTGCTCACCTT
CTTCAGTTACTCCATTGCTCCACGCATGGAGAAAAACATTAGCAAGGTCAAAGTCAGTATCTCTAAGCAGTGGACCCCAG
GTGCTTTTAACAAGTCCGTTGAACTGCCTGTGGAGATCTGGAGCAGCAGCCACATGTTTCCCAGTGCAGAGAAAGTACTC
GGAACGCTGGACACCATTTTCCTCTTCTCCTGTGCTGTGGGCCTTCTCATCAGCGGTATCTCGCCGATCGGCTAAATTTG
CGATGGGTTCTATCTTGTGGCATGTGCTTTTCCGCATTAGTGGTGTTCATCTTTGGCACTCTCATGGAACAGCTGCATTT
CTACAAGGGGCTGTGCTGCAGCCCGGGGATTGTTGAATGGCCTGCTGCCATCCACCGGCTGGCCCCGCGTGGTTTTTGTT
ACCGGCAACTAGTTTGGGAAAGCTGGAGTTGTTTTTGGTCTCTGGAGTGCCGGTGCCTCAGTGGGCAATATTTTGGGAGC
ATGTCTAGCTTCTTCCGTTCTGCAGTATGGTTATGAGTATGTCTTCCTGGTGATGCTAGCTGTGCAGTTTGCTGGTGGGA
CCATCATCTTCTTTGGACTCTTGGTATCACCAGAAGAAATCGGTCCCTCAGATATCGAGACAGAAGAAAATTTTGAAGAA
GACTCACACAGGCCATGAATTAATGGTGCTGAAAATGAAGAAGAAGCTGAGCCTAATTATTCAATCCAAGAAGGCAATAC
TGTGACCCAAGTCAAGGCAATAAACTTCTACCAGGCTTGTGGCCTTCCCGGAATTATAGCATATTCACTGGCCTATCGGT
GCTTGAAAGTA

Alignment

ORF - retro_btau_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AWPRIFQRGALLSRFSHHHMVVFLLTFFSYSLLHASRKTFSNVKVSISKQWTPSAFNKSTELLPVEIWSS
          AWP.IFQRG..LS.FSHHH.V..LLTFFSYS......K..S.VKVSISKQWTP.AFNKS.EL.PVEIWSS
Retrocopy AWPSIFQRGTVLSQFSHHHVVTSLLTFFSYSIAPRMEKNISKVKVSISKQWTPGAFNKSVEL-PVEIWSS

Parental  NHLFPSAEEATLFLGMLDTIFLFSYAVGLFISGI-VGDRLNLRWVLSFGMCSSALVVFVFGTLTEWLHFY
          .H.FPSAE.....LG.LDTIFLFS.AVGL.ISGI...DRLNLRWVLS.GMC.SALVVF.FGTL.E.LHFY
Retrocopy SHMFPSAEKV---LGTLDTIFLFSCAVGLLISGI<LADRLNLRWVLSCGMCFSALVVFIFGTLMEQLHFY

Parental  NKGLYCSLWIV-NGLLQSTGWPCVVAVMGNWFGKAGRGVVFGLWSACASVGNILGACLASSVLQYGYEYA
          .KGL.CS..IV.NGLL.STGWP.VV.V.GN.FGKAG..VVFGLWSA.ASVGNILGACLASSVLQYGYEY.
Retrocopy -KGLCCSPGIV>NGLLPSTGWPRVVFVTGN*FGKAG--VVFGLWSAGASVGNILGACLASSVLQYGYEYV

Parental  FLVTAAVQFAGGIIIFFGLLVSPEEIGIPGIETEDNFEEDSHRPLINGAENEDEAEPNYSIQEGNTVTQV
          FLV..AVQFAGG.IIFFGLLVSPEEIG...IETE.NFEEDSHRP.INGAENE.EAEPNYSIQEGNTVTQV
Retrocopy FLVMLAVQFAGGTIIFFGLLVSPEEIGPSDIETEENFEEDSHRP*INGAENEEEAEPNYSIQEGNTVTQV

Parental  KAISFYQACCLPGVIAYSLAYACLKL
          KAI.FYQAC.LPG.IAYSLAY.CLK.
Retrocopy KAINFYQACGLPGIIAYSLAYRCLKV

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	17.09 RPM
ERP005899_muscle	0.00 RPM	38.48 RPM
SRP017611_brain	0.00 RPM	17.81 RPM
SRP017611_kidney	0.00 RPM	32.36 RPM
SRP017611_liver	0.00 RPM	16.69 RPM
SRP030211_testis	0.00 RPM	19.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1471 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1471 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012239	1 retrocopy	retro_btau_1471 ,
Canis familiaris	ENSCAFG00000003973	1 retrocopy	retro_cfam_2207,
Mus musculus	ENSMUSG00000029924	1 retrocopy	retro_mmus_3670,
Ictidomys tridecemlineatus	ENSSTOG00000010929	1 retrocopy	retro_itri_1795,
Tursiops truncatus	ENSTTRG00000009525	1 retrocopy	retro_ttru_921,