RetrogeneDB ID: retro_mdom_1386

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:230329430..230330735(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHSRP
• Ensembl ID: ENSMODG00000001952
• Aliases: None
• Description: KH-type splicing regulatory protein [Source:HGNC Symbol;Acc:6316]

Sequence

>retro_mdom_1386
ACAACAGTGAATAACAGCACTCCAGATTTTGGTTTTGGGGGCCAAAAGAGACAGTTGGAAGATGGAGATCAACCTGAGAG
CAAGAAACTGGCAGCCCAAGGCGATTCTCTCAGTTCTCTACTTGGGCCTATTCATCCTCCTCCCTGGTCTTCAATGACAG
AAGAGTACCGTGTTCCTGATGGCAGGGTGGGACTAATCATTGGCAGAGGTGGTGAACAGATCAACAAGATCCAGCAGGAC
TCAGGCTGCAAAGTACAGATCTCACCAGACAGTGGCGGCTTACCTGAGCGAAGTGTGTCACTGACAGGAGCCCCGGAATC
AGTGCAGAAGGCAAAGATGATGTTAGATGACATTGTATCCCGGGGCCGAGGTGGTCCTCCTGGACAGTTCCATGATAATT
CAAATGGGGGTCAGAATGGCACAGTGCAGGAGATCATGATTCCTGCAGGAAAAGCAGGACTGGTGATTGGCAAAGGCGGG
GAGACCATTAAGCAGCTGCAGGAGCAAGCTGGAGTGAAGATGATTTTAATTCAAGATGGATCCCAAAATACCAATGTGGA
CAAACCTCTCCGGATTATTGGTGACCCATATAAAGTATAGCAAGCCTGTGAGATGGTGATGGACATCCTCCGAGAACGTG
ACCAAGGAGGCTTTGGGGACCGGAATGAATATGGATCCCAGATTGGTGGTGGGATAGATGTGCCAGTACCCAGACATTCT
GCTGGTGTGGTCATTGGCCGGAGTGGAGAAATGCTCAAAAAAATACAAAGTGATGCTGGTGTCCGAATACAATTCAAACA
AGATGATGAAACAGGTCCTGAGAAGATAGCCCACATCATGGGACCCCCAGACCGGTGTGAGCATGCTGCCAGAATCATCA
ATGACCTCCTCCAGAGTTTAAGGAGTGGTCCCCCCGGACCTCTTGGGGGCCCAGGCATGCTTCCTGGAGGGAGGGGCCGA
GGCCGAGGCCAGGGTAACTGGGGACCTCCTGGTGGAGAGATGACTTTCTCCATTCCAACTCACAAGTGTGGGCTTGTTAT
TGGTAGAGGTGGGGAGAAGGTGAAAGCCATAAATCAACAAACAGGCGCCTTTGTGGAGATCTCTCAGCAGCTCCCACCAA
ATGGGGACCCTAATTTCAAGCTCTTCATCATCCGGGGATCCCCTCAGCAAATTGACCATGCCAAGCAGCTTATTGAGGAG
AAAATTGAGGGTCCTCTCTGTCCAGTTGGACCAGGTCCTGGGGGACCAGGTCCTGCTGGTCCAATGGGGCCCTTCAACCC
AGGACCTTTTAACCAGGGGCCTCCA

Alignment

ORF - retro_mdom_1386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.05 %
• Parental protein coverage: 65.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTVNNSTPDFGFGGQKRQLEDGDQPESKKLAAQGD--FSIRPIYHTPR-SSLTEEYRVPDGMVGLIIGRG
          TTVNNSTPDFGFGGQKRQLEDGDQPESKKLAAQGD...S.....H.P..SS.TEEYRVPDG.VGLIIGRG
Retrocopy TTVNNSTPDFGFGGQKRQLEDGDQPESKKLAAQGDSLSSLLGPIHPPPWSSMTEEYRVPDGRVGLIIGRG

Parental  GEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNSNGGQNG
          GEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNSNGGQNG
Retrocopy GEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGGPPGQFHDNSNGGQNG

Parental  TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL
          TVQEIMIPAGKAGLVIGKGGETIKQLQE.AGVKMILIQDGSQNTNVDKPLRIIGDPYKV.QACEMVMDIL
Retrocopy TVQEIMIPAGKAGLVIGKGGETIKQLQEQAGVKMILIQDGSQNTNVDKPLRIIGDPYKV*QACEMVMDIL

Parental  RERDQRGFGDRNEYGSRIGGGIDGPEPKNSVGGGIGPSGKMIQKIQRGAGVPKQFKQDDGTGPEKIAHIM
          RERDQ.GFGDRNEYGS.IGGGID.P.P..S.G..IG.SG.M..KIQ..AGV..QFKQDD.TGPEKIAHIM
Retrocopy RERDQGGFGDRNEYGSQIGGGIDVPVPRHSAGVVIGRSGEMLKKIQSDAGVRIQFKQDDETGPEKIAHIM

Parental  GPPDRCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG
          GPPDRCEHAARIINDLLQSLRSGPPGP.GGPGM.PGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG
Retrocopy GPPDRCEHAARIINDLLQSLRSGPPGPLGGPGMLPGGRGRGRGQGNWGPPGGEMTFSIPTHKCGLVIGRG

Parental  GENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAG
          GE.VKAINQQTGAFVEIS.QLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL..............
Retrocopy GEKVKAINQQTGAFVEISQQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLXXXXXXXXXXXXXX

Parental  PMGPFNPGPFNQGPP
          .MGPFNPGPFNQGPP
Retrocopy XMGPFNPGPFNQGPP

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_1386 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1386 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016627	1 retrocopy	retro_cjac_460,
Homo sapiens	ENSG00000088247	1 retrocopy	retro_hsap_4142,
Macaca mulatta	ENSMMUG00000005597	1 retrocopy	retro_mmul_1185,
Monodelphis domestica	ENSMODG00000001952	1 retrocopy	retro_mdom_1386 ,
Otolemur garnettii	ENSOGAG00000008073	1 retrocopy	retro_ogar_884,
Pan troglodytes	ENSPTRG00000010364	1 retrocopy	retro_ptro_2814,