RetrogeneDB ID: retro_mdom_1075

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:526042417..526043707(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF38
• Ensembl ID: ENSMODG00000002665
• Aliases: None
• Description: ring finger protein 38 [Source:HGNC Symbol;Acc:18052]

Sequence

>retro_mdom_1075
ATGCAACCATGGAAGATGACATCAAATAGGCAGCCTCCTTCAGTTCGACCCAATCAGCATCATTTCTCAGGGGAATGATG
CAACACACCTGCACGCAACAGAAGTCCTCCTGTTAGGCGCCAGAGAGGAAGGAGGGATCGTCTCTCTCAACATAATTCCA
TTAGTCAGGATGAAATCTATCACCATCTTTCATATGGACAGCAGCAAGCAATAGAGGAACCCCGAGCCTTCCATCCTTCG
AATGTATCCCCACGTATGTTGCATCCTACTGCTCACCCACCACAGCAGAATGCAGTGATGGTTGACATACATGAACAGCT
TCATCAAGGCACAGTCCCAGTTTCTTATACTGTAACAACTGTTGCTCCACATGGGATTCCACTTTGTACTGGTCAGCACA
TCCCTGCTTGTAATATACAGCAGGTTCCAGGATGCTCTGTGGTTTTCAGTGGACAGCACCTCCCAGTCTGTAGTGTGCCT
CCTCCAATGCTTCAGGCATGTTCAGTTCAGCACTTGCCAGTACCATATGCTGCATTCCCACCTCTTATTTCTAGTGATCC
ATTTCTTTTACATCCGCCTCACCTTTCTCCACATCCTCCTCCTCATTTGCCACCACCTGGCCAGTTTGTACCCTTCCAAA
CACAGCAATCACAATCGCCATTACAGAGGATAGAAAATTAAGTTGAACTCTTGGGAGAACACCTTCCTGTAGGAGGCTTT
ACTTATCCTGCATCGGCCCATCCTCCAACATTACCTCCATCAGCCCTTCTCCAGTTCTTAATACACGATCCTTTGCACCA
GGAGGTATCTTTTGGAGTACCTTATCCTCCATTTATGCCTCGAAGACTTACAGGACATAGTAGATATCAATCCCAGCAAC
CAATACCGCCTCCCCCTTATCATCCCAGTCTCCTACCATATGTACTATCAATGCTTCCAGTGCCACCTGCAATAGGTCCA
GCCTTCAGCTTTGAATTGGATGGAGTAGATGGAGAAGTAGAAAATTATGAGGCATTACTAAATCTGGCAGAATGACTAGA
AGCTAAGCCACGTGGATTAACAAAAGCAGATACCGAATAGCTTCCTTCTTACCGGTTCAATCCTATCAACCACCAGTCAG
AGCAGACTTTGTGCGTAGTATGCATGTGTGATTTTGAGTCAAGGCAGCTACTTAGAGTCTTACCCTGTAACCATGAGTTC
CATGCCAAGTATGTTGATAAATGGCTTAAGGCAAATTGTACCTGCCCAATTTGTCGAGCTGATGCATCGGAAGTACATCG
TGATTCAGAA

Alignment

ORF - retro_mdom_1075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPWEMTSNRQPPSVRPNQHHFSGERCNTPARNRRSPPVRRQRGRRDRLSRHNSISQDENYHHLSYGQQQ
          M.PW.MTSNRQPPSVRPNQHHFSGE.CNTPARNR.SPPVRRQRGRRDRLS.HNSISQDE.YHHLSYGQQQ
Retrocopy MQPWKMTSNRQPPSVRPNQHHFSGE*CNTPARNR-SPPVRRQRGRRDRLSQHNSISQDEIYHHLSYGQQQ

Parental  AIEEPRAFHPPNVSPRMLHPAAHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACNT
          AIEEPRAFHP.NVSPRMLHP.AHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACN.
Retrocopy AIEEPRAFHPSNVSPRMLHPTAHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACNI

Parental  QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPHHPPHLPPPGQF
          QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPH.PPHLPPPGQF
Retrocopy QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPHPPPHLPPPGQF

Parental  VPFQTQQSRSPLQRIENEVELLGEHLPVGGFTYPASAHPPTLPPSAPLQFLTHDPLHQEVSFGVPYPPFM
          VPFQTQQS.SPLQRIEN.VELLGEHLPVGGFTYPASAHPPTLPPSA.LQFL.HDPLHQEVSFGVPYPPFM
Retrocopy VPFQTQQSQSPLQRIEN*VELLGEHLPVGGFTYPASAHPPTLPPSALLQFLIHDPLHQEVSFGVPYPPFM

Parental  PRRLTGRSRYRSQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELDVEDGEVENYEALLNLAERLGEA
          PRRLTG.SRY.SQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELD..DGEVENYEALLNLAE.L.EA
Retrocopy PRRLTGHSRYQSQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELDGVDGEVENYEALLNLAE*L-EA

Parental  KPRGLTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC
          KPRGLTKAD.E.LPSYRFNP.NHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAK.VDKWLKAN.TCPIC
Retrocopy KPRGLTKADTE*LPSYRFNPINHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKYVDKWLKANCTCPIC

Parental  RADASEVHRDSE
          RADASEVHRDSE
Retrocopy RADASEVHRDSE

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_1075 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1075 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
Bos taurus	ENSBTAG00000005519	1 retrocopy	retro_btau_396,
Callithrix jacchus	ENSCJAG00000010299	1 retrocopy	retro_cjac_2182,
Monodelphis domestica	ENSMODG00000002665	1 retrocopy	retro_mdom_1075 ,