RetrogeneDB ID: retro_mdom_1236

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:46778603..46779459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000015696
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F7E0Q7]

Sequence

>retro_mdom_1236
CGAGTGAACAACTGCATTGGAGGTGTCATCCTTTTCCATGAGACTTTCTCTCAGAAAGTTGGTGATGGTCGTCCCTTTCC
CAAAGTCCAAGGCCAAGGGTGGTGTTGTGGGCATCAAGGTGGACAAAGGTATAGTGCCCCTGGCAGGGACCAATGGGGAG
ACTACCACCCAAGGTCTGGATGGTCTAGCTGAGCGCTGTGTCCAGTATAAGAAGGATGGGGCCGACTTTGCCAAGTGGTG
TTGTGTGCTGAAGATTGGGGAAAATACACCTTCTCCACTTGCCGTCTTGAAGAATGCCAGTGTGCTGTCCTGATATGCCA
GCATTTTCCAACAGACTGGCATTGTCCCCATTGTGGAGCCAGAGATCCTCCCTGATGGAGAACATGATCTGAAGTGTTGC
CAGTATGTCCCTGAGAAGGTTCTGGCCGCTGTCTGTAAAGCTTTGAGTAACCACCATATCTATCTGGAGGGGACCTTGCT
GTAGGCTAACATGGTCACTCCTGGGCATGCTTGTACCCAGAAATATTCGCATGAGGAGATTGCAATAGCAACCGTGACTG
CCCTTTGCTAGACTGTGCCTCCTGCAGTCACTGGTATCACCTTCCTGTCTGGGGATCAGAATGAGGAGAATGTTTCCATC
AATCTCAATGCCATCAGTACCAGCCCCTAGCAAAAGCCATAGGCCCTGACCTTTTCTTATGGCATGCCCTGTAGGCATCT
GCCCTCAAGACCTGGGGTGGAAAGAAGGAAAAACATCCAGGCTGCCCAGAAGGAATATGTTAAGCAGGTCTTAGCTAATA
GCCAGGCTGCTCAAGTCAAGTATACTCCATCAGGAAAGTCAGGAGCTGCAGCCAGT

Alignment

ORF - retro_mdom_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.43 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RVNSCIGGVILFHETLYQKADDGRPF-PKVIKAKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLAERCAQ
          RVN.CIGGVILFHET..QK..DGRPF.PK..KAKGGVVGIKVDKG.VPLAGTNGETTTQGLDGLAERC.Q
Retrocopy RVNNCIGGVILFHETFSQKVGDGRPF>PKS-KAKGGVVGIKVDKGIVPLAGTNGETTTQGLDGLAERCVQ

Parental  YKKDGADFAKWRCVLKIGENTPSPLAIMENANVLARYASICQQNGIVPIVEPEILPDGEHDLKCCQYVTE
          YKKDGADFAKW.CVLKIGENTPSPLA...NA.VL..YASI.QQ.GIVPIVEPEILPDGEHDLKCCQYV.E
Retrocopy YKKDGADFAKWCCVLKIGENTPSPLAVLKNASVLS*YASIFQQTGIVPIVEPEILPDGEHDLKCCQYVPE

Parental  KVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGITFLSGGQSE
          KVLAAV.KALS.HHIYLEGTLL..NMVTPGHACTQKYSHEEIA.ATVTAL..TVPPAVTGITFLSG.Q.E
Retrocopy KVLAAVCKALSNHHIYLEGTLL*ANMVTPGHACTQKYSHEEIAIATVTALC*TVPPAVTGITFLSGDQNE

Parental  EDASINLNAINTCPLHKPWALTFSYG-RALQASALKTWGGKKE-NVQAAQEEYVKRALANSQAAQGKYTP
          E..SINLNAI.T.P..KP.ALTFSYG..AL.ASALKTWGGKKE.N.QAAQ.EYVK..LANSQAAQ.KYTP
Retrocopy ENVSINLNAISTSP*QKP*ALTFSYG<HAL*ASALKTWGGKKE>NIQAAQKEYVKQVLANSQAAQVKYTP

Parental  SGKSGAAAS
          SGKSGAAAS
Retrocopy SGKSGAAAS

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1236 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1236 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 32 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	ENSMODG00000014418	2 retrocopies	retro_mdom_1752, retro_mdom_393,
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,