RetrogeneDB ID: retro_mmus_3266

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:40039890..40040768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lztfl1
• Ensembl ID: ENSMUSG00000025245
• Aliases: Lztfl1, 5530402H04Rik, 6130400H19Rik, AI414725, AW048545
• Description: leucine zipper transcription factor-like 1 [Source:MGI Symbol;Acc:MGI:1934860]

Sequence

>retro_mmus_3266
GAGTTGGGCCTAAATGACCACCATCAAAATGAGGTCATTAATTACATGTGTTTTTCTTGTCCAGAAAGAAGCTGGAGACA
TAAAAGGGTAGATTCCTGCTTTCAAGACCTCAAGCACAGCATGCTTGTAAAGGAGACTTTCATCATAGATGAGGTTTCAA
AAGTCCTAAATGGGCTGCAGGCTATGGTACACAGTGAAGTGCAGTCCGAGCTCATCAATACAGCTTACATCAATGTCCTG
CTCCTATGGCAGCTGTTCTCACAAGCTGAGAAGTGGTGTCTAAAGCTACAGACAGGCATCTCTGAACTTGAAAGCAGACA
ACTATTAGAACAAGTTGCTGAATTTGAAAGGGTAGAATTTGCATCTTCAAATAAAAAGTTCATCATAGCTATCAAAAAGC
CTAAACTTGTTCTGATTTAGGAAGGTGGAACAACAGAGCTGCTAAACAAGGAAAATTTAAGACTTCAACAAGACAATGAA
AAACTAAAGTCAAGGCTGAAGACCATTGAAATACAGGCTGTAAATGCTCTGGATGAAAAGTCAAAATTGGAAGGAGCACT
TCAAGATTTACAGCTCGATCAAGAAAACCAACAGGACTTTCAAAGGCCCAAGACTTGGATGACTTGGAAAACATAGTTGC
AACTGTTAGGACTGAATTTCAGAAGACACTTAATCACAAGACAGAAAACCAAAATTCTTTGGAAGAGAACCTAGCAGAAG
CCAAACATGACCTCCTCAGAGTACGGGAGCAGCTGAGCATGGCTAAAAAGGAGTTAGAGAAGAAATTCCAACAAACAGCA
GCTTATGGAAACATGAAAGAGATTCTCACCAAAAAGAATGATCTAATCAAGGACCTATGGAAAACACTGATAAAATAT

Alignment

ORF - retro_mmus_3266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELGLNEHHQNEVINYMRFARSKRGLRLKTVDSCFQDLKDSRLVEETFTIDEVSEVLNGLQAVVHSEVESE
          ELGLN.HHQNEVINYM.F....R..R.K.VDSCFQDLK.S.LV.ETF.IDEVS.VLNGLQA.VHSEV.SE
Retrocopy ELGLNDHHQNEVINYMCFSCPERSWRHKRVDSCFQDLKHSMLVKETFIIDEVSKVLNGLQAMVHSEVQSE

Parental  LINTAYTNVLLLRQLFSQAEKWYLKLQTDISELENRELLEQVAEFEKAEFVSSSKKPIIDITKPKLVPIN
          LINTAY.NVLLL.QLFSQAEKW.LKLQT.ISELE.R.LLEQVAEFE..EF.SS.KK.II.I.KPKLV.I.
Retrocopy LINTAYINVLLLWQLFSQAEKWCLKLQTGISELESRQLLEQVAEFERVEFASSNKKFIIAIKKPKLVLI*

Parental  EGGTTELLNKEILRLQQENEKLKSRLKTIEIQAVNALDEKSKLERVLQDLQLDQENQQD-LLKAQDLDDL
          EGGTTELLNKE.LRLQQ.NEKLKSRLKTIEIQAVNALDEKSKLE..LQDLQLDQENQQD.L.KAQDLDDL
Retrocopy EGGTTELLNKENLRLQQDNEKLKSRLKTIEIQAVNALDEKSKLEGALQDLQLDQENQQD<LSKAQDLDDL

Parental  ENTVATLRSEFQKTLNDKTENQKSLEENLAAAKHDLLRVQEQLSMAEKELEKKFQQTAAYRNMKEILTKK
          EN.VAT.R.EFQKTLN.KTENQ.SLEENLA.AKHDLLRV.EQLSMA.KELEKKFQQTAAY.NMKEILTKK
Retrocopy ENIVATVRTEFQKTLNHKTENQNSLEENLAEAKHDLLRVREQLSMAKKELEKKFQQTAAYGNMKEILTKK

Parental  NDQIKDLRKRLAKY
          ND.IKDL.K.L.KY
Retrocopy NDLIKDLWKTLIKY

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	36.42 RPM
SRP007412_cerebellum	0.00 RPM	20.49 RPM
SRP007412_heart	0.00 RPM	9.65 RPM
SRP007412_kidney	0.00 RPM	14.23 RPM
SRP007412_liver	0.00 RPM	5.05 RPM
SRP007412_testis	0.18 RPM	38.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3266 was not detected

EST

No EST(s) were mapped for retro_mmus_3266 retrocopy.

TSS

No TSS is located nearby retro_mmus_3266 retrocopy 5' end.

Lab

retro_mmus_3266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3266 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003899	1 retrocopy	retro_chof_1935,
Echinops telfairi	ENSETEG00000013761	1 retrocopy	retro_etel_1726,
Loxodonta africana	ENSLAFG00000010237	1 retrocopy	retro_lafr_155,
Mus musculus	ENSMUSG00000025245	3 retrocopies	retro_mmus_1834, retro_mmus_3266 , retro_mmus_3276,
Procavia capensis	ENSPCAG00000009783	1 retrocopy	retro_pcap_313,