RetrogeneDB ID: retro_ocun_1550

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018699:8373864..8374581(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSOCUG00000006329
• Aliases: None
• Description: aldolase A, fructose-bisphosphate (ALDOA), mRNA [Source:RefSeq mRNA;Acc:NM_001082238]

Sequence

>retro_ocun_1550
AAAGGGTTGGATGGGCTGTCTGAGCATTGTGCCCAGTATAAGAAAGATGGAACCGACTTCGCCAAGTGGCGTTGTGTGCT
GAAAATTGGGGAACACACCCCGTCAGCCCTCGCCATCATGGAGAATGCCAACGTCTTGGCCCATTATGCCAGCATCTGCC
AGCAGAATGGCATTTTGCTCATTGTGGAGCCTGAAATCCTCCCTGGTGGGGACCACGACCTGAAGCAATGCCAATATGTC
ACTGAGAAGGTGCTGGCAGCTGTCTACAAGGCTCTGAGTGATCACCACATCTACCTGGAAGGCACCTTGCTGAAGCCCAA
TAGGGTAACCCCAAGCCATGCCTGCACCCAAAAGTATTCTCACGAGGAGATTGCCATGGCAACTGTCACGGCGCTGCACC
GCACTGTGCCCCTCGCTGTCACTGGAATTACCTTCCTGTCTGGAGGTCAGAGTGAGGAGGAGGTATCCATCAATCTCAAG
GCCATCAACAAGTGCCCCCTACTGAAGCTGTGGGCCCTGACCTTCTCCTACGGCCGTGCCCTGCAGGCCCCGGCCCTGAA
GGACTGGGGCGGGAAGAAGGAGAACCTGAAGGCTGCCCAAGAGGAGTAAGTGAAGCGGACCCTGGCCAACAGCCTCGCCT
GCCAAGCGAAGTACACCCCGAGTGGTCAGGCCGGGGCCGCAGCCAGCGAGTCCCTCTTCATCTCTAAGCACGCCTAC

Alignment

ORF - retro_ocun_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDG
          .GLDGLSE.CAQYKKDG.DFAKWRCVLKIGEHTPSALAIMENANVLA.YASICQQNGI..IVEPEILP.G
Retrocopy KGLDGLSEHCAQYKKDGTDFAKWRCVLKIGEHTPSALAIMENANVLAHYASICQQNGILLIVEPEILPGG

Parental  DHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAV
          DHDLK.CQYVTEKVLAAVYKALSDHHIYLEGTLLKPN.VTP.HACTQKYSHEEIAMATVTAL.RTVP.AV
Retrocopy DHDLKQCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNRVTPSHACTQKYSHEEIAMATVTALHRTVPLAV

Parental  TGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALAN
          TG.TFLSGGQSEEE.SINL.AINKCPLLK.WALTFSYGRALQA.ALK.WGGKKENLKAAQEE.VKR.LAN
Retrocopy TGITFLSGGQSEEEVSINLKAINKCPLLKLWALTFSYGRALQAPALKDWGGKKENLKAAQEE*VKRTLAN

Parental  SLACQGKYTPSGQAGAAASESLFISNHAY
          SLACQ.KYTPSGQAGAAASESLFIS.HAY
Retrocopy SLACQAKYTPSGQAGAAASESLFISKHAY

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	0.11 RPM	961.27 RPM
SRP017611_kidney	0.00 RPM	658.82 RPM
SRP017611_liver	0.00 RPM	85.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1550 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1550 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550 ,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,