RetrogeneDB ID: retro_btau_535

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:66555903..66556479(-)
• Located in intron of: ENSBTAG00000019621

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSBTAG00000007865
• Aliases: GNPDA1, GNPI
• Description: Glucosamine-6-phosphate isomerase 1 [Source:UniProtKB/Swiss-Prot;Acc:A4FV08]

Sequence

>retro_btau_535
ATGAAGCACAACATTCTGGACCACTATTCTCAGGCCAGTGAGTACTCAGCCAAATATATCAGGAACTGCATCACCAGTTT
AGTGCAAGACCAGACAAGTACTTCACTCTGGGGCTCCCCTCTGGGAGCACCCCCACTTGGCTGCTACAAGAAGCTGATTG
AGTACTATAAGAATGAAGACCTGTCCTTCCAATATTGAAGACTTTCAACATGGATGAGTATGTGGGCCTTCCTTGAGACC
ACTGGGAGAGTTACCACTCCTTCATGTGAGACACCTTCCTCAAACACATTGACATCCTCCCAGAAAACACCCAAATTCTG
GATGGGAATGTAGTTGGCCTACAGGCTGAGTGTGATGCCTTTGAAGAGACAATCAAGGCTGCAGGTAGGGATTGAGCTGT
TTGTTGGAGGGATGGGCCTTGATGAACACATTGCCTTTTACAAGTCAGGCTCCAGTCTGTTGTCCAGGACCCATGTGAAG
ATGCTGGCCATGGACACCATCCTGGCCAGTGCTAGGTTCTTCAGTGGTAATCTCACCAAGGTGCCCACCATGGCCCTGAC
AGTGGGCATGGGCACT

Alignment

ORF - retro_btau_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.06 %
• Parental protein coverage: 66.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKLIILDHYSQASEWAAKYIRNRII-QFNPGPDKYFTLGLPTGSTP-LGCYKKLIEYYKNGDLSFKY-VK
          MK..ILDHYSQASE..AKYIRN.I..QF...PDKYFTLGLP.GSTP.LGCYKKLIEYYKN.DLSF.Y..K
Retrocopy MKHNILDHYSQASEYSAKYIRNCIT<QFSARPDKYFTLGLPSGSTP>LGCYKKLIEYYKNEDLSFQY<LK

Parental  TFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILDGNAADLQAECDAFEEKIKAAG-GIELFVG
          TFNMDEYVGLP.DH.ESYHSFM...F.KHIDI.PENT.ILDGN...LQAECDAFEE.IKAAG.GIELFVG
Retrocopy TFNMDEYVGLP*DHWESYHSFM*DTFLKHIDILPENTQILDGNVVGLQAECDAFEETIKAAG>GIELFVG

Parental  GIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDLAKVPTMALTVGVGT
          G.G.D.HIAF...GSSL.SRT.VK.LAMDTILA.ARFF.G.L.KVPTMALTVG.GT
Retrocopy GMGLDEHIAFYKSGSSLLSRTHVKMLAMDTILASARFFSGNLTKVPTMALTVGMGT

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	12.98 RPM
ERP005899_muscle	0.00 RPM	32.04 RPM
SRP017611_brain	0.00 RPM	10.10 RPM
SRP017611_kidney	0.00 RPM	68.99 RPM
SRP017611_liver	0.00 RPM	10.27 RPM
SRP030211_testis	0.03 RPM	13.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_535 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535 ,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,