RetrogeneDB ID: retro_mdom_1935

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:188878920..188880166(-)
• Located in intron of: ENSMODG00000014700

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A23
• Ensembl ID: ENSMODG00000002023
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23 [Source:HGNC Symbol;Acc:19375]

Sequence

>retro_mdom_1935
ATCCTACAAGAGGGGGATATAGACCAAGATGGGGGCCTGACCCTTGAAGAATTCACCAGCTACCTACAGGAACATGAGAG
ACGACTGCTGCTTATGTTCCACAGCCTGGACGGGAACCAGGATGGCCATATAGATGCCTCAGAAATTCAGGAAAGCTTCC
AAACCCTGGGTGTTTCCATCTCTTTGCAGCAGGCTGAAAAGATTCTGCACAGCATGGACCGTGATGGGACAATGACCATT
GACTGGCAAGAATGGCGAGACCACTTCCTGCGGCAGCCCCTGGAGAACATGGAGGATGTACTGAAGTTCTGGAAACACTC
AACGGTCCTGGACATAGGGGAATGTCTGACAGTGCCAGATGAGTTCTCAGAACAGGAGAAGCTATCAGGCATGTGGTGGA
AACAGCTGGTGGCAGGAGCTGTGGCAGGGGCCGTGTCACGGACAGGCACAGCCCCCCCTTAACTGGCTAAAGGTTTTCAT
GCATGTTCATGCCTCCAAGAACAACCAGTTGAATGTCCTAGGAGGGCTGCGGAACATGGTCCAAGAGGGTGGCATCTGCT
CTTTGTGGCGTGGAAATGGCATCAATGTACTGAAGATCACACCTGAATCTGCCATCAAATTCATGGCATATGAGCAGATC
AAGTGGGCGATTTGGGGGCAGCAGGACATGCTGCGGGTGCAGGAGCGCTTTGTGGCAGGGTCCCTGGCCGGGGCCACAGC
CCAAACCATCATCTATCCCGTGGAGGTGCTGAAGACATGGCTAACCCTCTGTCGAACTGGCCAGTACAAAGGATTACTGG
ATTGCGCACGGCAGATCCTAGAGCAGGAGGGGCCCAGAGCCTTCTACAAGGGCTACCTGCCCAATGTCTTGGGCATTATC
CCCTATGCAGGAATCGACCTGGCTGTCTATGAGACCCTGAAGAACAGGTGGCTCCAGCAGGACAGCCACCACTCAGCTGA
CCCAGGGATCCTTGTGCTGTTGGCCTGCGGCACCATTTCCAGTACCTGTGGCCAGATCACCAGCTATCCCTTGGCTCTGG
TCCGAACTCGTATACAAGCTCAGGCTTCCATCGAGGGTGCCCCAAAGCTCACCATGCTGGGCCTCTTCCGTCACATCCTT
TCCCGAGAGGGGGTGTGGGGCCTGTACTGAGGCATCACCCCCAACTTCATGAAAGTGATTCCGGCTGTGAGCATCTCCTA
TATCGTCTATGAGAACGTGAAACAGGCCCTGGGGGTCACCACCAGG

Alignment

ORF - retro_mdom_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILQEGDIDQDGGLTLEEFTRYLQEHERRLLLMFHSLDRNQDGHIDASEIQESFQALGVSISLQQAEKILH
          ILQEGDIDQDGGLTLEEFT.YLQEHERRLLLMFHSLD.NQDGHIDASEIQESFQ.LGVSISLQQAEKILH
Retrocopy ILQEGDIDQDGGLTLEEFTSYLQEHERRLLLMFHSLDGNQDGHIDASEIQESFQTLGVSISLQQAEKILH

Parental  SMDRDGTMTIDWQEWRDHFLLQPLENMEDVLKFWKHSTVLDIGECLTVPDEFSEQEKLSGMWWKQLVAGA
          SMDRDGTMTIDWQEWRDHFL.QPLENMEDVLKFWKHSTVLDIGECLTVPDEFSEQEKLSGMWWKQLVAGA
Retrocopy SMDRDGTMTIDWQEWRDHFLRQPLENMEDVLKFWKHSTVLDIGECLTVPDEFSEQEKLSGMWWKQLVAGA

Parental  VAGAVSRTGTAP-LDRLKVFMQVHASKNNQLNVLGGLRNMVQEGGIRSLWRGNGINVLKIAPESAIKFMA
          VAGAVSRTGTAP.L..LKVFM.VHASKNNQLNVLGGLRNMVQEGGI.SLWRGNGINVLKI.PESAIKFMA
Retrocopy VAGAVSRTGTAP>LNWLKVFMHVHASKNNQLNVLGGLRNMVQEGGICSLWRGNGINVLKITPESAIKFMA

Parental  YEQIKWAIRGQQETLRVQERFVAGSLAGATAQTIIYPMEVLKTRLTLRRTGQYKGLLDCARQILEQEGPR
          YEQIKWAI.GQQ..LRVQERFVAGSLAGATAQTIIYP.EVLKT.LTL.RTGQYKGLLDCARQILEQEGPR
Retrocopy YEQIKWAIWGQQDMLRVQERFVAGSLAGATAQTIIYPVEVLKTWLTLCRTGQYKGLLDCARQILEQEGPR

Parental  AFYKGYLPNVLGIIPYAGIDLAVYETLKNRWLQQDSHHSADPGILVLLACGTISSTCGQIASYPLALVRT
          AFYKGYLPNVLGIIPYAGIDLAVYETLKNRWLQQDSHHSADPGILVLLACGTISSTCGQI.SYPLALVRT
Retrocopy AFYKGYLPNVLGIIPYAGIDLAVYETLKNRWLQQDSHHSADPGILVLLACGTISSTCGQITSYPLALVRT

Parental  RMQAQASIEGAPQLTMLGLFRHILSREGVWGLYRGIAPNFMKVIPAVSISYVVYENMKQALGVTTR
          R.QAQASIEGAP.LTMLGLFRHILSREGVWGLY.GI.PNFMKVIPAVSISY.VYEN.KQALGVTTR
Retrocopy RIQAQASIEGAPKLTMLGLFRHILSREGVWGLY*GITPNFMKVIPAVSISYIVYENVKQALGVTTR

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_1935 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1935 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002023	1 retrocopy	retro_mdom_1935 ,
Monodelphis domestica	ENSMODG00000017305	1 retrocopy	retro_mdom_1534,