RetrogeneDB ID: retro_mmus_2000

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:170285034..170285877(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084013
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hax1
• Ensembl ID: ENSMUSG00000027944
• Aliases: Hax1, HAX-1, HSP1BP-1, Hs1bp1, SIG-111, Silg111, mHAX-1s
• Description: HCLS1 associated X-1 [Source:MGI Symbol;Acc:MGI:1346319]

Sequence

>retro_mmus_2000
ATGAGCGTCTTTGATCTTTTCCGAGGCTTTTTCGGCTTTCCTGGACCTCGGAGCCACAGAGATCCTTTTTTTGGAGGGAT
GACTCGAGATGATGACGACGATGATGATGATGATGATGACGAAGCGGAGGAAGACAGAGGCGCGTGGGGTTGAGAGAGCT
ATGCGTTTGATGGTTCTCAGCCTCCAGAGGAATTCGGTTTCAGCTTCAGCCCCAGGGGAGGGATGCGATTCCACGGCAAC
TTTGGCTTTGATGATCTAGTACGAGATTTTAATAGCATCTTCAGCGAGATGGGGGCCTGGACCTTGCCTTCCCACTCTCC
TGAACTTCCAGGTCCTGAGTCAGAAACACCTGGTGAGAGACTGCGGGAGGGGCAGACACTACGAGACTCAATGCTTAAGT
ACCCAGATAGTCACCAACCCAGGATCTTTGAGGGGGTCTTGGAGAGTCATGCAAAACCTGAATCCCCAAAACCAGCTCCA
GATTGGGGGTCCCAGGGACCTTTTCATAGGTTGGATGATACATGGCCTGTGAGTCCCCATTCTAGAGCCAAAGAGGACAA
AGATCTTGATTCCCAGGTTTCCCAGGAAGGTCTGGGTCCACTTCTTCAACCCCAGCCCAAATCGTATTTCAAAAGTATCT
CTGTGACCAAGATCACTAAGCCAGATGGGACAGTGGAGGAACGCCGCACTGTGGTAGACAGTGAGGGCCGGAGGGAGACC
ACAGTGACCCATCAAGAAGCCCATGACAGTTCCAGAAGTGATCCAGACTCTCAGAGATCTTCAGCTTTGGATGATCCCTT
TTCCATTCTGGATTTGCTACTAGGACGTTGGTTTCGGTCCCGA

Alignment

ORF - retro_mmus_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVFDLFRGFFGFPGPRSHRDP-FFGGMTRDDDDDDDDDDEAEEDRGAWGRESYAFDGSQPPEEFGFSFS
          MSVFDLFRGFFGFPGPRSHRDP.F.G..............EAEEDRGAWG.ESYAFDGSQPPEEFGFSFS
Retrocopy MSVFDLFRGFFGFPGPRSHRDPFFGGMTRXXXXXXXXXXXEAEEDRGAWG*ESYAFDGSQPPEEFGFSFS

Parental  PRGGMRFHGNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGPESETPGERLREGQTLRDSMLKYPDSHQP
          PRGGMRFHGNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGPESETPGERLREGQTLRDSMLKYPDSHQP
Retrocopy PRGGMRFHGNFGFDDLVRDFNSIFSEMGAWTLPSHSPELPGPESETPGERLREGQTLRDSMLKYPDSHQP

Parental  RIFEGVLESHAKPESPKPAPDWGSQGPFHRLDDTWPVSPHSRAKEDKDLDSQVSQEGLGPLLQPQPKSYF
          RIFEGVLESHAKPESPKPAPDWGSQGPFHRLDDTWPVSPHSRAKEDKDLDSQVSQEGLGPLLQPQPKSYF
Retrocopy RIFEGVLESHAKPESPKPAPDWGSQGPFHRLDDTWPVSPHSRAKEDKDLDSQVSQEGLGPLLQPQPKSYF

Parental  KSISVTKITKPDGTVEERRTVVDSEGRRETTVTHQEAHDSSRSDPDSQRSSALDDPFSILDLLLGRWFRS
          KSISVTKITKPDGTVEERRTVVDSEGRRETTVTHQEAHDSSRSDPDSQRSSALDDPFSILDLLLGRWFRS
Retrocopy KSISVTKITKPDGTVEERRTVVDSEGRRETTVTHQEAHDSSRSDPDSQRSSALDDPFSILDLLLGRWFRS

Parental  R
          R
Retrocopy R

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	0.05 RPM	12.08 RPM
SRP007412_cerebellum	0.09 RPM	15.68 RPM
SRP007412_heart	0.03 RPM	10.09 RPM
SRP007412_kidney	0.15 RPM	31.34 RPM
SRP007412_liver	0.05 RPM	25.31 RPM
SRP007412_testis	0.23 RPM	41.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2000 was not detected

EST

No EST(s) were mapped for retro_mmus_2000 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_83887	402 libraries	201 libraries	367 libraries	79 libraries	23 libraries

The graphical summary, for retro_mmus_2000 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2000 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000 , retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,