RetrogeneDB ID: retro_ocun_1266

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:30451237..30451907(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSOCUG00000016963
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]

Sequence

>retro_ocun_1266
GACGGAGACTTCTCTTCCAAATATGAGAAGACCTTCAACATGGACGAGTACGTCGGCCTGCCTCATGACCGCTGGCAGAG
TAGCCACTCCTTCACGCAGATCAACTTCTTCAAGCACATTGACATTCACTCTGCGAAACCCCACTTGCTGGATGGGGGTG
CAGCTGCCCTTCTGGCCGAGTATGATGCCTTTGAAGAGAAGATCAAGGCTGCAGGTGGGGGTGAGCTCTTTATTGGGGGC
ACAGTCCTGATAAATATGTTGACTGCAATGCACCACACTCCAGCCTGGTGTCCAGGATCCATGTAAAGGAATTGGCCATG
GACACAATCCTGGCCAGCGTTAGGTTCCTCAGTGGAAATCCGGCCAAGGTGCCCACCAGGGCTGCGATGGTGGGCATGAA
CACTGTTGTGGATGCTAGAGAGGTGATGATCCTCATCTCTGCTGCCCACCAGGCCTTTGCTCTGTCAAAGAGTGTAGAGG
AGGGGGTGAGCCACATATGGATGTTGTCTGCCTTCTGGCAGTAGCCACATGGCATGTTTGTAGGTGACAAGGATACCACC
TTGGAGCTGAAAGTGAAGACTTTCAAGTATTTAAACATATCCATGGACCACTTGTATGCTATCAAGGAGAAAGAAATTGA
GGAAAACCAGGCTTTTAAGAACCATATAGC

Alignment

ORF - retro_ocun_1266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.09 %
• Parental protein coverage: 79.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGDLSFKYVKTFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILDGNAADLQAECDAFEEKIKA
          .GD.S.KY.KTFNMDEYVGLP.D...S.HSF...NFFKHIDIH....H.LDG.AA.L.AE.DAFEEKIKA
Retrocopy DGDFSSKYEKTFNMDEYVGLPHDRWQSSHSFTQINFFKHIDIHSAKPHLLDGGAAALLAEYDAFEEKIKA

Parental  AGGIELFVGGI-GPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDLAKVPTMALTVGVGTVMDA
          AGG.ELF.GG...PD.....N.P.SSLVSR..VK.LAMDTILA..RF..G..AKVPT.A..VG..TV.DA
Retrocopy AGGGELFIGGT<SPDKYVDCNAPHSSLVSRIHVKELAMDTILASVRFLSGNPAKVPTRAAMVGMNTVVDA

Parental  REVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHNKLV
          REVMILI..AH.AFAL.K..EEGV.H.W..SAF.Q.P...FV.D.D.TLELK...VK.FK.L....N...
Retrocopy REVMILISAAHQAFALSKSVEEGVSHIWMLSAFWQ*PHGMFVGDKDTTLELK---VKTFKYL----NISM

Parental  DPLYSIKEKEIEKSQSSK-KPYS
          D.LY.IKEKEIE..Q..K..PYS
Retrocopy DHLYAIKEKEIEENQAFK<EPYS

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
SRP017611_brain	0.00 RPM	45.75 RPM
SRP017611_kidney	0.00 RPM	123.55 RPM
SRP017611_liver	0.00 RPM	16.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1266 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1266 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Oryctolagus cuniculus	ENSOCUG00000016963	1 retrocopy	retro_ocun_1266 ,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,