RetrogeneDB ID: retro_mmus_1488

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:12950780..12951464(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zwint
• Ensembl ID: ENSMUSG00000019923
• Aliases: Zwint, 2010007E07Rik, 2600001N01Rik, D10Ertd749e, Zwint-1
• Description: ZW10 interactor [Source:MGI Symbol;Acc:MGI:1289227]

Sequence

>retro_mmus_1488
AATGCTGTTGCGATGAAAGAGGCTCTGGCTGAGGCAGCAGCCTTTCTAGAACCTGCTGCAGGCTTGCAGGAGGAAGCAGA
ACTGCCTGCCAAGATCATGGGGGAGTTCGTAGGAACTCTCGGAAGAAAGACAAGCTGCTGCTTTGTAGCCAGCTTCAAGT
AGTGAACTTCTTACAGACGTCTCTGCCTCAGGAGGATACTGACCAGAATCCAGATGCATTGGCTTCTGAAGATGCAAGTC
GGCAAAAGGCAACTGGAACTAAGGAGCTGTGGAAGGCATGAAGGCCACATACATGGATCATGTGGAGGTCATAAAATGTG
CTCTATCTGAGGCCTTCCCCCAGGTCAAAGAGGCTCACAGGAAGTACGCAGAGCTTCAGACTGCTTTTGAGCAACTCAAG
GCTAAGAAGCGAGTCCTTGAGGAGAAACTTCAATCAGTTCAGAAGCAGTGGATGCTGCGGCAGGAGCATGTGCAGAATAC
GACAAAGACTTCTGCAGAGGCAAAGAGACCCTGGAAAAGGGCCCTGGAGAAGCTTGGCAGATCCCATCAGGAACTTGAAA
CCTTGACGCAGCAAGCAGGACAGGAACAGGAGAAGCTGCGGAGGACCAGAGCTACCTCCAGCTGCAGAATAAGCTGGTCA
TCTCTGAGGGCAAGGCTGAGGACAAAGATGTCAAAGCTGAGGCT

Alignment

ORF - retro_mmus_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NAVATKEVLAEAAAILEPV-GLQEEAELPAKIMEEFM-RNSRKKDKLL-CSQLQVVNFLQTFLAQEDTEQ
          NAVA.KE.LAEAAA.LEP..GLQEEAELPAKIM.EF..RNSRKKDKLL.CSQLQVVNFLQT.L.QEDT.Q
Retrocopy NAVAMKEALAEAAAFLEPAAGLQEEAELPAKIMGEFV<RNSRKKDKLLLCSQLQVVNFLQTSLPQEDTDQ

Parental  SPDALASEDASRQKATETKEQWK-DMKATYMDHVDVIKCALSEALPQVKEAHRKYTELQKAFEQLEAKKR
          .PDALASEDASRQKAT.TKE.WK..MKATYMDHV.VIKCALSEA.PQVKEAHRKY.ELQ.AFEQL.AKKR
Retrocopy NPDALASEDASRQKATGTKELWK<GMKATYMDHVEVIKCALSEAFPQVKEAHRKYAELQTAFEQLKAKKR

Parental  VLEEKLQLAQKQWVLQQKRLQNLTKISAEVKRRRKRALEKLDGSHQELETLKQQAGQEQEKLQR-NQSYL
          VLEEKLQ..QKQW.L.Q...QN.TK.SAE.KR..KRALEKL..SHQELETL.QQAGQEQEKL.R..QSYL
Retrocopy VLEEKLQSVQKQWMLRQEHVQNTTKTSAEAKRPWKRALEKLGRSHQELETLTQQAGQEQEKLRR<DQSYL

Parental  QLLCSLQNKLVISEGKAEDKDVKGRA
          QL....QNKLVISEGKAEDKDVK..A
Retrocopy QL----QNKLVISEGKAEDKDVKAEA

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	0.02 RPM	713.71 RPM
SRP007412_cerebellum	0.00 RPM	405.77 RPM
SRP007412_heart	0.00 RPM	37.51 RPM
SRP007412_kidney	0.00 RPM	61.54 RPM
SRP007412_liver	0.00 RPM	42.74 RPM
SRP007412_testis	0.59 RPM	46.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1488 was not detected

EST

No EST(s) were mapped for retro_mmus_1488 retrocopy.

TSS

No TSS is located nearby retro_mmus_1488 retrocopy 5' end.

Lab

retro_mmus_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002655	1 retrocopy	retro_btau_239,
Echinops telfairi	ENSETEG00000007793	1 retrocopy	retro_etel_261,
Mus musculus	ENSMUSG00000019923	3 retrocopies	retro_mmus_1488 , retro_mmus_2611, retro_mmus_997,
Rattus norvegicus	ENSRNOG00000048682	2 retrocopies	retro_rnor_1211, retro_rnor_1306,
Tarsius syrichta	ENSTSYG00000010283	1 retrocopy	retro_tsyr_1005,
Tursiops truncatus	ENSTTRG00000002204	1 retrocopy	retro_ttru_1193,