RetrogeneDB ID: retro_mdom_516

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:125640690..125641737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN11
• Ensembl ID: ENSMODG00000003120
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 11 [Source:HGNC Symbol;Acc:9644]

Sequence

>retro_mdom_516
CTTCCTCGTGGGGGAAAGCCAGAGCCACTCCGAGAATTTTATTCTTTCTGCACAGGGGACGATAAAGGCGAGAGTAATGA
TGGCAAATCAAAAATGACGCACTTCAAGATTCGCTGTCAGCATCTGAAATATGATGTTGGTGGAGGAGAGAAGTTTGCCT
CTTTAACAGACTTTGTAGAGCATTACAAGAAGAACCCTATGGTAGAAACTTTGGGTACAGTTCTACAGCTCAAGCAGCCT
CTGAATACAACTCGTATCAATGCTGCAGAGATTGAAAGCTGGGTGAGAGAATTAAGCTAATTAGCGGAGACCACAGATAA
AGTGAAACAAGGGTTTTGGGAAGAATTTGGGACTCTCCAACAGCAGGAATGCAAGCTCCTCTATAGTCGTAAAGAAGGTC
AGCAGCAAGAAAATAAAAACAAAAACATATATAAGAATATTTTGCCCTTTGATCATACCAGGGTCGTCCTACATGATGGG
GATCAAAATGAACCAGTTTCAGATTATATTAATGCAAATATTACCATTCCTGAATTTGAGACCAAATGCAACACAAAACC
CAAAAAGAATTATATTGCAACCCAAGGCTGTCTACAGAACACAGTAAACGACTTCTGGAGAATGGTGTTCCAGGAGAATT
CACGAGTTATTGCCATGACAATGAAAGAAGTAGAGAGAGGGAAGAGTAAATGTGTCAAGTACTGGCCTAATGAATATGCT
CTAAAGGAATATGGGACTATGCGTGTTAGGAATGTCAAAGAAAGTGCTTCTCATGTCCATACTTTTGGATAACTAAAACT
CTCTAAGTTTGGACAAGGGGACACTGAGAAAACTGTGTGGCAGTACCATTTTGGAACCTGGCCGGATCACGGTGTGCCCA
TTGACCCTAGGGGTCTTCTGGACTTTTTAGAAGCCATCCATAACAAGCAGGAGAGCATTCCTGATGCAGGCTCTGTGGTG
TTGTATTGCAGTGCTGGGATTGGCAGGACAGGAACTTTCATTGTGATTGACATCCTTATTGACATTATCAGAGAAAAAGG
TGTGGAT

Alignment

ORF - retro_mdom_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 59.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQDLKYDVGGGEKFDSLTDLVEHYKKNPMVET
          L.R.....P.....S..TGDDKGESNDGKSK.TH..IRCQ.LKYDVGGGEKF.SLTD.VEHYKKNPMVET
Retrocopy LPRGGKPEPLREFYSFCTGDDKGESNDGKSKMTHFKIRCQHLKYDVGGGEKFASLTDFVEHYKKNPMVET

Parental  LGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKN
          LGTVLQLKQPLNTTRINAAEIES.VRELS.LAETTDKVKQGFWEEF.TLQQQECKLLYSRKEGQ.QENKN
Retrocopy LGTVLQLKQPLNTTRINAAEIESWVRELS*LAETTDKVKQGFWEEFGTLQQQECKLLYSRKEGQQQENKN

Parental  KNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMV
          KN.YKNILPFDHTRVVLHDGD.NEPVSDYINANI..PEFETKC.N.KPKK.YIATQGCLQNTVNDFWRMV
Retrocopy KNIYKNILPFDHTRVVLHDGDQNEPVSDYINANITIPEFETKC-NTKPKKNYIATQGCLQNTVNDFWRMV

Parental  FQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGAMRVRNVKESAAHDYTLRELKLSKVGQGNTERTV
          FQENSRVI.MT.KEVERGKSKCVKYWP.EYALKEYG.MRVRNVKESA.H..T...LKLSK.GQG.TE.TV
Retrocopy FQENSRVIAMTMKEVERGKSKCVKYWPNEYALKEYGTMRVRNVKESASHVHTFG*LKLSKFGQGDTEKTV

Parental  WQYHFRTWPDHGVPTDPGGVLDFLEEVHHKQESIPDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVD
          WQYHF.TWPDHGVP.DP.G.LDFLE..H.KQESIPDAG.VV..CSAGIGRTGTFIVIDILIDIIREKGVD
Retrocopy WQYHFGTWPDHGVPIDPRGLLDFLEAIHNKQESIPDAGSVVLYCSAGIGRTGTFIVIDILIDIIREKGVD

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	0.33 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	0.79 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_516 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_516 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501, retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516 ,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,