RetrogeneDB ID: retro_mdom_554

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:282723063..282724491(-)
• Located in intron of: ENSMODG00000013060

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA5
• Ensembl ID: ENSMODG00000017826
• Aliases: None
• Description: karyopherin alpha 5 (importin alpha 6) [Source:HGNC Symbol;Acc:6398]

Sequence

>retro_mdom_554
GAAAGTCCTATTCAGGATCCAGTTATCAGCTCTACTGTACTTGTTCCTGAGGAAGAAGTTATTACTGCTGATATGGTGCA
GATGATTTTCTCTGATGATGCTGACCAACAGCTTACAGCAACACAAAAGTTTTGAAAGTTGCTTTCTAAAGAACCTAACC
AACCTATAGATGAAGTTATACAAAAACCAGGAGTTGTACAGAGATTTGTGAAGTTTCTTGAAAGAAACGAAAATTGTACT
TTGCAGTTTGAAGCTGCATGGGCTTTAACTAATATGGTATCTGGAACATTTCTACTCACCAAAGTGGTAATTCAAATTGG
AGCTGTTCCAATTTTTATCAAACTCCTCAATTCAGAACATGAAGATGTACAGGAACAGGCAGTATGGACACTTGGTAATA
TTGCTAGTGATAATGCAGAATGCAGAGGCTTTGTTCTGAATTGTGGAATTCTTCCCCCTCTTTTAGAATTACTGACAAAT
TCAAAAAGACTTACAACAACTCGAAATGCTGTATAGGCACTCTCAAATTTATGTAGAGGCAAGAACCCACCTCCAGATTT
CAGTAAGGTGTCACCTTGCTTAAATGTCCTGTCAAGATTATTATTTAGCAGTGACCCAGATGTATTAGCAGATGCTTGTT
GGGCCCTTTCTTATCTTTCTGATGGACCCAATGACAAAATCCAAGCAGTCATTGACTCTGGAGTCTGTCAAAGATTGGTG
GAACTTTTGATGCACAATGATTATAAAGTGGTATCACCTGTATTAAGAGCTGTTGGTAATATTGTGAAAGGGGATGATAT
TCAAACACAGGTAATTCTGAATTGTTCTGCTTTACCCTGCCTCTTACATTTACTGAGTAGTCCAAAAGAATCAATTAGAA
AAGAGGCTTGCTGGACTGTATCTAACATTACAGCAGGAAATAGAGCACAGATTCAGGCTGTCATAGATGCAAATATCTTT
CCTGTGTTGATTGAAATTCTTCAGAAAGCTGAATTTCATACCAGAAAAGAGGCAGCATAGGCCATAACCAATGCAACATC
TGGAGGCACTCCAGAACAGATACGGTATCTGGTAGCATTAGGCTGTATTAAACCTCTCTGTGACCTTTTGACTGTGATGG
ATTCCAAAATAGTCCAGGTGGCTTTAAATGGCCTTGAAGATATTTTACGACTTGGAGAGCAAGAATCTAGACAAAATGAA
ATGAACATCAATCCATACTGTGCTCTCATTGAAGAAGCATATGGTCTGGATAAAACTGAGTTTCTTCAAAGCCATGAAAA
TCAAGAGATCTACCAAAAGGCTTTTGATCTAATTGAACACTACTTTGGGGTGGAAGATGAAGATGCCAACATTGTCCCTC
AGGTGGATGAAAACCAGTAACAATTTGTTTTCCAACAGCAGGAAGCACCAATGGAAGGATTTCAGTTA

Alignment

ORF - retro_mdom_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 88.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESPIQDPDISSTVPVPEEEVITADMVQMIFSDDADQQLTATQKVKKEHFFKPNPPIDEVIQKPGVVQRFV
          ESPIQDP.ISSTV.VPEEEVITADMVQMIFSDDADQQLTATQK..K.....PN.PIDEVIQKPGVVQRFV
Retrocopy ESPIQDPVISSTVLVPEEEVITADMVQMIFSDDADQQLTATQKF*KLLSKEPNQPIDEVIQKPGVVQRFV

Parental  KFLERNENCTLQFEAAWALTNIASGTFLHTKVVIETGAVPIFIKLLNSEHEDVQEQAVWALGNIAGDNAE
          KFLERNENCTLQFEAAWALTN..SGTFL.TKVVI..GAVPIFIKLLNSEHEDVQEQAVW.LGNIA.DNAE
Retrocopy KFLERNENCTLQFEAAWALTNMVSGTFLLTKVVIQIGAVPIFIKLLNSEHEDVQEQAVWTLGNIASDNAE

Parental  CRDFVLNCGILPPLLELLTNSNRLTTTRNAVWALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA
          CR.FVLNCGILPPLLELLTNS.RLTTTRNAV.ALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA
Retrocopy CRGFVLNCGILPPLLELLTNSKRLTTTRNAV*ALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA

Parental  DACWALSYLSDGPNDKIQAVIDSGVCRRLVELLMHNDYKVVSPALRAVGNIVTGDDIQTQVILNCSALPC
          DACWALSYLSDGPNDKIQAVIDSGVC.RLVELLMHNDYKVVSP.LRAVGNIV.GDDIQTQVILNCSALPC
Retrocopy DACWALSYLSDGPNDKIQAVIDSGVCQRLVELLMHNDYKVVSPVLRAVGNIVKGDDIQTQVILNCSALPC

Parental  LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFRTRKEAAWAITNATSGGT
          LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEF.TRKEAA.AITNATSGGT
Retrocopy LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFHTRKEAA*AITNATSGGT

Parental  PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQESRQNEMNINPYCALIEEAYGLDKIE
          PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLE.ILRLGEQESRQNEMNINPYCALIEEAYGLDK.E
Retrocopy PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLEDILRLGEQESRQNEMNINPYCALIEEAYGLDKTE

Parental  FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQQQFVFQQQEAPMEGFQL
          FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQ.QFVFQQQEAPMEGFQL
Retrocopy FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQ*QFVFQQQEAPMEGFQL

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	0.48 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	1.77 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_554 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_554 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Monodelphis domestica	ENSMODG00000017826	1 retrocopy	retro_mdom_554 ,
Otolemur garnettii	ENSOGAG00000011924	1 retrocopy	retro_ogar_2991,