RetrogeneDB ID: retro_mmus_1429

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:3730509..3731022(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095834
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tdgf1
• Ensembl ID: ENSMUSG00000032494
• Aliases: Tdgf1, CR1, cripto
• Description: teratocarcinoma-derived growth factor 1 [Source:MGI Symbol;Acc:MGI:98658]

Sequence

>retro_mmus_1429
ATGGGGTACTTCTCATCCAGTGTGGTTTTGCTTGTGGCCATTTCCAGTGTGTTTGAATTTGGACCCGTTGCTGGGAGAGA
CCTTGCCATCAGAGATAACAGCATTTGGGACCAGAAAGAACCTGCCGTACGCGATCGGTCTTTCCAGTTCGTGCCTTCCG
TGGGGATACAGAACAGTAAGTCGCTTAATAAAACTTGCTGTCTGAATGGAGGGACTTGCATCCTGGGGTCCTTCTGTGCC
TGCCCTCCTTCCTTCTATGGACGCAACTGTGAACATGATGCTCGCAAAGAGCACTGTGGGTCTATCCTCCATGGCACCTG
GCTGCCCAAGAAGTGTTCCCTGTGCAGATGCTGGCACGGCCAGCTCCACTGTCTTCCTCAGACCTTTCTACCTGGCTGTG
ATGGTCACGTGATGGACCAGGACCTCAAAGCATCCAGGACTCTGTGTCAAACGCCGTCTGTGATGACCACTTTTATGCTA
GCTGGCGCCTGCCTTTTTCTAGATATGAAAGTT

Alignment

ORF - retro_mmus_1429 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGYFSSSVVLLVAISSAFEFGPVAGRDLAIRDNSIWDQKEPAVRDRSFQFVPSVGIQNSKSLNKTCCLNG
          MGYFSSSVVLLVAISS.FEFGPVAGRDLAIRDNSIWDQKEPAVRDRSFQFVPSVGIQNSKSLNKTCCLNG
Retrocopy MGYFSSSVVLLVAISSVFEFGPVAGRDLAIRDNSIWDQKEPAVRDRSFQFVPSVGIQNSKSLNKTCCLNG

Parental  GTCILGSFCACPPSFYGRNCEHDVRKEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCDGHVMDQ
          GTCILGSFCACPPSFYGRNCEHD.RKEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCDGHVMDQ
Retrocopy GTCILGSFCACPPSFYGRNCEHDARKEHCGSILHGTWLPKKCSLCRCWHGQLHCLPQTFLPGCDGHVMDQ

Parental  DLKASGTPCQTPSVTTTFMLAGACLFLDMKV
          DLKAS.T.CQTPSV.TTFMLAGACLFLDMKV
Retrocopy DLKASRTLCQTPSVMTTFMLAGACLFLDMKV

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	0.30 RPM
SRP007412_cerebellum	0.04 RPM	1.43 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1429 was not detected

EST

No EST(s) were mapped for retro_mmus_1429 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_47085	887 libraries	71 libraries	89 libraries	23 libraries	2 libraries
TSS #2	TSS_47086	981 libraries	51 libraries	12 libraries	23 libraries	5 libraries

The graphical summary, for retro_mmus_1429 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_1429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002174	3 retrocopies	retro_cjac_1594, retro_cjac_4151, retro_cjac_938,
Felis catus	ENSFCAG00000014508	1 retrocopy	retro_fcat_714,
Homo sapiens	ENSG00000241186	7 retrocopies	retro_hsap_1999, retro_hsap_2393, retro_hsap_2709, retro_hsap_3415, retro_hsap_3956, retro_hsap_4737, retro_hsap_4804,
Gorilla gorilla	ENSGGOG00000003453	5 retrocopies	retro_ggor_1447, retro_ggor_1815, retro_ggor_2307, retro_ggor_2943, retro_ggor_2990,
Loxodonta africana	ENSLAFG00000009140	4 retrocopies	retro_lafr_1037, retro_lafr_1067, retro_lafr_757, retro_lafr_871,
Microcebus murinus	ENSMICG00000016492	1 retrocopy	retro_mmur_635,
Macaca mulatta	ENSMMUG00000003088	6 retrocopies	retro_mmul_1744, retro_mmul_2290, retro_mmul_2560, retro_mmul_742, retro_mmul_770, retro_mmul_967,
Mustela putorius furo	ENSMPUG00000015167	1 retrocopy	retro_mputfur_961,
Mus musculus	ENSMUSG00000032494	3 retrocopies	retro_mmus_1429 , retro_mmus_1544, retro_mmus_1908,
Nomascus leucogenys	ENSNLEG00000006143	6 retrocopies	retro_nleu_1649, retro_nleu_2124, retro_nleu_2179, retro_nleu_2317, retro_nleu_2519, retro_nleu_535,
Otolemur garnettii	ENSOGAG00000017039	1 retrocopy	retro_ogar_2611,
Pan troglodytes	ENSPTRG00000014854	7 retrocopies	retro_ptro_1333, retro_ptro_1749, retro_ptro_1831, retro_ptro_2319, retro_ptro_2685, retro_ptro_3153, retro_ptro_3194,
Tarsius syrichta	ENSTSYG00000013609	2 retrocopies	retro_tsyr_295, retro_tsyr_574,
Tursiops truncatus	ENSTTRG00000017299	1 retrocopy	retro_ttru_441,