RetrogeneDB ID: retro_mdom_1672

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:122903264..122904091(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSMODG00000021167
• Aliases: None
• Description: septin 7 [Source:HGNC Symbol;Acc:1717]

Sequence

>retro_mdom_1672
TGTTGTCTATACTTCATTGCCCTTTCAGGTCATGGCCTCAAGCCTCTGGACATTTGAGTTCATGAAACGCTTGCATGACA
AGGTGAATGTCATTCCGCTCATTGCCAAAGCAGACATGCTGACTCCTGAAGAATGCCAGCAGTTTAAGAAGCAGATATGA
AAGAAATTCAAGAGCACAAAATAAAAATATATGAGTTTCCAGAAACAGATGCTGAGGAAGAAAATAAGCTTGCTAAAAAG
ATAAAGGACTGTTTGCCTCTTGCTGTGGTTGGTAGCAATACTATCATTGAAGTTAATGGCAAAAGGGTCCAAGGAAGACA
GTATCCTTGAGGTGTTGCAGAAGTTGAAAAATGGTGAACATTGCGATTTCACATTTCTAAGAAACATTTTGATAAGAACC
CACATGCAGGACCTGAAGAATGTGACGAGCAATGTGCACTACGAGAACTATAGGAGCCAGAAGCTGGCAGCTGTGACGTA
CAATAGTGTAGATAACAACAAGAACAAAGGGCAGCTGACCAAGAGCACTCTGGCCCAAATGGAGGAAGAAAGAAGGGAAC
CTGTAGCGAAGAATAAGAAGATGGAGATGGAGAATGGAGCAAGTGTTCGAGCTGAAGGTCAAAGAAAAGGTTCAGAAGCT
CAAGGACTTGGAAGCCAAGCTGCAGTGGCATCATGAGCAGATGAAGAAGAACCTGGAAGCCCAGCACAAGGAACTGGAGG
AGAAGCGGCGCCAGTTTGAGGATGACAAAGCCAACTGGGAAGTTCAGCAGTGGATCTTAGAGCAACAAAACACTTCCAGA
ACTTTGGAAAAGAACAAGAAGAAAGGG

Alignment

ORF - retro_mdom_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 62.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CCLYFIAPSGHGLKPLDI-EFMKRLHDKVNVIPLIAKADTLTPEECQQFKKQI-MKEIQEHKIKIYEFPE
          CCLYFIA.SGHGLKPLDI.EFMKRLHDKVNVIPLIAKAD.LTPEECQQFKKQI.MKEIQEHKIKIYEFPE
Retrocopy CCLYFIALSGHGLKPLDI>EFMKRLHDKVNVIPLIAKADMLTPEECQQFKKQI<MKEIQEHKIKIYEFPE

Parental  TDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVE-NGEHCDFTILRNMLIRTHMQD
          TD.EEENKL.KKIKD.LPLAVVGSNTIIEVNGKRV.GRQYP.GVAEVE.NGEHCDFT.LRN.LIRTHMQD
Retrocopy TDAEEENKLAKKIKDCLPLAVVGSNTIIEVNGKRVQGRQYP*GVAEVE>NGEHCDFTFLRNILIRTHMQD

Parental  LKDVTSNVHYENYRSRKLAAVTYNSVDNNKNKGQLTKSPLAQMEEERREHVAKMKKMEME-MEQVFEMKV
          LK.VTSNVHYENYRS.KLAAVTYNSVDNNKNKGQLTKS.LAQMEEERRE.VAK.KKMEME.MEQVFE.KV
Retrocopy LKNVTSNVHYENYRSQKLAAVTYNSVDNNKNKGQLTKSTLAQMEEERREPVAKNKKMEME>MEQVFELKV

Parental  KEKVQKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDDKANWEAQQRILEQQNTSRTLEKNKKKG
          KEKVQKLKD.EA.LQ..HEQMKKNLEAQHKELEEKRRQFEDDKANWE.QQ.ILEQQNTSRTLEKNKKKG
Retrocopy KEKVQKLKDLEAKLQWHHEQMKKNLEAQHKELEEKRRQFEDDKANWEVQQWILEQQNTSRTLEKNKKKG

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_1672 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1672 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
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Equus caballus	ENSECAG00000022693	1 retrocopy	retro_ecab_650,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000003104	1 retrocopy	retro_mdom_93,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672 ,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,
Tursiops truncatus	ENSTTRG00000016197	1 retrocopy	retro_ttru_329,