RetrogeneDB ID: retro_mdom_726

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:243585717..243586224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSMODG00000019364
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_mdom_726
TTCCGTCCCGCCTGCGCCATGCTGTCCCTGGACTTCTTGGACGATGTGCAGAGGATGAACAAGCGGCAGCTGTATTATCA
AGTCCTAGACTTTGGGATGATCATTTCTTCAGCTTTAATGATCTGGAAAGGACTAATGGTAGTAACTGGAAGTGAAAGCC
CAATTGTAGTGGTGCACAGTGGAAGCATGGAACCTGCACTTCACAGAGGAGCTCTTCTCTTTTTAACCAATCGAATTGAA
GATCCCATAAGAGTAGGAGAGATTATTGTCTTTAAGATAGAAGGAAGGGAAATTCCAATTGTTCACCAAGTGTTGAAAAT
TCACGAAAGGCAAGATGGACATATCAAGTTTTTGACCAATGGAGACAATAATGCTGTTGATGATCGAGGGTTATATAAGC
AAGGGCAGGTCTGGCTAGAGAAGAAAGATGTAGTAGGATGAGCAAGAGGATTTGTTCTTTATATTGGAATTGTGATGATT
CTTATGAATGACTATCTTAAATTTAAG

Alignment

ORF - retro_mdom_726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.12 %
• Parental protein coverage: 66.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRPARAMLSLDFLDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVVTGSESPIVVVLSGSMEPAFHRG
          FRPA.AMLSLDFLDDV.RMNKRQLYYQVL.FGMI.SSALMIWKGLMVVTGSESPIVVV.SGSMEPA.HRG
Retrocopy FRPACAMLSLDFLDDVQRMNKRQLYYQVLDFGMIISSALMIWKGLMVVTGSESPIVVVHSGSMEPALHRG

Parental  DLLFLTNRIEDPIRVGEIVVFKIEGREIPIVHRVLKIHERQDGHIKFLTKGDNNAVDDRGLYKQGQLWLE
          .LLFLTNRIEDPIRVGEI.VFKIEGREIPIVH.VLKIHERQDGHIKFLT.GDNNAVDDRGLYKQGQ.WLE
Retrocopy ALLFLTNRIEDPIRVGEIIVFKIEGREIPIVHQVLKIHERQDGHIKFLTNGDNNAVDDRGLYKQGQVWLE

Parental  KKDVVGRARGFVPYIGIVTILMNDYPKFK
          KKDVVG.ARGFV.YIGIV.ILMNDY.KFK
Retrocopy KKDVVG*ARGFVLYIGIVMILMNDYLKFK

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	50.54 RPM
SRP007412_cerebellum	0.00 RPM	48.32 RPM
SRP007412_heart	0.00 RPM	103.46 RPM
SRP007412_kidney	0.00 RPM	123.78 RPM
SRP007412_liver	0.00 RPM	158.60 RPM
SRP007412_testis	0.00 RPM	83.68 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_726 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_726 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Erinaceus europaeus	ENSEEUG00000015328	2 retrocopies	retro_eeur_314, retro_eeur_412,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Macaca mulatta	ENSMMUG00000011486	1 retrocopy	retro_mmul_2343,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726 ,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Ictidomys tridecemlineatus	ENSSTOG00000019948	1 retrocopy	retro_itri_206,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,