RetrogeneDB ID: retro_mmus_997

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:18038559..18039300(+)
• 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_997
CAGCAGAGCGTGGCGGCCATGGAGAATTCCGCTGTGGCAGCAAAAGAGGTCCTGGCTGAGGTAGCAGGCATTCTAGAACA
TGTAGGCTTGCAGGAAGAAACAGAGCTGCCTCCCAAGAACATGGAGGAGTTTGTGAGGAACTCTCAGAAGAAAGACAAGC
TGCTCTGTAGCCAAAGCTTGTACTTGAAAGTAGTGAACTTCTTACAGAATCTTCTGACTCAGAAGGATAATAGAGCTCAG
AACCCAGACACTTTGGTTTCTGAAAACGTAAGTTGACAGAAGGCAACTGAAGCTAAGGAACACTGGAAGGAACTGAAGGC
CACATACCTGGATCACGTGGACAACCCAAGCTGTGCCCTGACCCAGGCCTTACCCCAGGTTAAAGAGGCTCAAAGGAAGT
ACACAGAGCTTTGGAAGGCTTTTGAACAACTTGAGGCTAGGAAGCAAGTACTTGAGAAACTTCAGTGAGCTCAGAAGCAG
TGGCAGCTGCAACAGAAGTGTTTACAGAGTCTGGCAGAGATTTCTGCATGGGGTAAAGGGAGGTCAGAAAAGAGCTCTGA
GAACCTTGACAGATCACACCAGGAACTTGGAACCTTGAAGCAGCATGCAGGATAGGCACAGGGGAAGCTGCAGTGGAATC
AGGCCTACCTCCAGCTGCTGGGTACCCTGCAGAATAAGCTGGCCATTGCTGAGGCAAAGATGTCACAGGACGACTTGCCC
TCCCACTCAAGTCTCCCTAAA

Alignment

ORF - retro_mmus_997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.11 %
• Parental protein coverage: 96.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKNAVAEKNNAVATKEVLAEAAAILEPVGLQEEAELPAKIMEEFMRNSRKKDKLLCSQ---LQVVNFLQT
          .....A..N.AVA.KEVLAE.A.ILE.VGLQEE.ELP.K.MEEF.RNS.KKDKLLCSQ...L.VVNFLQ.
Retrocopy QQSVAAMENSAVAAKEVLAEVAGILEHVGLQEETELPPKNMEEFVRNSQKKDKLLCSQSLYLKVVNFLQN

Parental  FLAQEDTE-QSPDALASEDASRQKATETKEQWKDMKATYMDHVDVIKCALSEALPQVKEAHRKYTELQKA
          .L.Q.D...Q.PD.L.SE..S.QKATE.KE.WK..KATY.DHVD...CAL..ALPQVKEA.RKYTEL.KA
Retrocopy LLTQKDNRAQNPDTLVSENVS*QKATEAKEHWKELKATYLDHVDNPSCALTQALPQVKEAQRKYTELWKA

Parental  FEQLEAKKRVLEEKLQLAQKQWVLQQKRLQNLTKISAEVKRRRKRALEKLDGSHQELETLKQQAGQEQEK
          FEQLEA.K.VL.EKLQ.AQKQW.LQQK.LQ.L..ISA..K.R.....E.LD.SHQEL.TLKQ.AG..Q.K
Retrocopy FEQLEARKQVL-EKLQ*AQKQWQLQQKCLQSLAEISAWGKGRSEKSSENLDRSHQELGTLKQHAG*AQGK

Parental  LQRNQSYLQLLCSLQNKLVISEGKAEDKDVKGRALTAK
          LQ.NQ.YLQLL..LQNKL.I.E.K....D........K
Retrocopy LQWNQAYLQLLGTLQNKLAIAEAKMSQDDLPSHSSLPK

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	0.09 RPM	46.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_997 was not detected

EST

No EST(s) were mapped for retro_mmus_997 retrocopy.

TSS

No TSS is located nearby retro_mmus_997 retrocopy 5' end.

Lab

retro_mmus_997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_997 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1306

---

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,