RetrogeneDB ID: retro_mmus_2862

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:99877818..99878334(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084319
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tpt1
• Ensembl ID: ENSMUSG00000060126
• Aliases: None
• Description: tumor protein, translationally-controlled 1 [Source:MGI Symbol;Acc:MGI:104890]

Sequence

>retro_mmus_2862
ATGATCATCTACCGGGACCTCATCAGCCATGACGAGCTGTTCTCCGACATCTACAAGATCCGGGAGATCGCGGACGGGCT
GTGCCTGGAGGTGGAGGGCAAGATGGTCAGTAGAACAGAGGGTGCCATCGATGACTCGCTCATCGGTGGAAATGCTTCCG
CTGAAGGTCCGGAGGGCGAAGGTACCGAAAGCACAGTAGTCACCGGTGTTGACATTGTCATGAACCATCACTTACAAGAA
ACCAGCTTCACAAAAGAGGCTTACAAAAAGTACATCAAAGACTACATGAAATCACTCAAAGGCAAACTTGAAGAGCAGAA
ACCAGAAAGAGTAAAGCCTTTTATGACTGGAGCTGCAGAGCAGATTAAGCACATCCTTGCTAATTTCAATAACTACCAGT
TTTTTATTGGTGAAAACATGAATCCAGATGGTATGGTTGCTCTCCTGGACTACCGTGAAGATGGTGTGACTCCATTCATG
ATTTTCTTTAAGGATGGCTTAGAGATGGAGAAATGT

Alignment

ORF - retro_mmus_2862 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MIIYRDLISHDELFSDIYKIREIADGLCLEVEGKMVSRTEGAIDDSLIGGNASAEGPEGEGTESTVVTGV
          MIIYRDLISHDELFSDIYKIREIADGLCLEVEGKMVSRTEGAIDDSLIGGNASAEGPEGEGTESTVVTGV
Retrocopy MIIYRDLISHDELFSDIYKIREIADGLCLEVEGKMVSRTEGAIDDSLIGGNASAEGPEGEGTESTVVTGV

Parental  DIVMNHHLQETSFTKEAYKKYIKDYMKSLKGKLEEQKPERVKPFMTGAAEQIKHILANFNNYQFFIGENM
          DIVMNHHLQETSFTKEAYKKYIKDYMKSLKGKLEEQKPERVKPFMTGAAEQIKHILANFNNYQFFIGENM
Retrocopy DIVMNHHLQETSFTKEAYKKYIKDYMKSLKGKLEEQKPERVKPFMTGAAEQIKHILANFNNYQFFIGENM

Parental  NPDGMVALLDYREDGVTPFMIFFKDGLEMEKC
          NPDGMVALLDYREDGVTPFMIFFKDGLEMEKC
Retrocopy NPDGMVALLDYREDGVTPFMIFFKDGLEMEKC

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	0.56 RPM	138.61 RPM
SRP007412_cerebellum	0.09 RPM	86.23 RPM
SRP007412_heart	2.21 RPM	376.27 RPM
SRP007412_kidney	2.37 RPM	341.53 RPM
SRP007412_liver	0.93 RPM	283.46 RPM
SRP007412_testis	0.73 RPM	182.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2862 was not detected

EST

No EST(s) were mapped for retro_mmus_2862 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_126353	62 libraries	45 libraries	452 libraries	348 libraries	165 libraries

The graphical summary, for retro_mmus_2862 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_2862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2862 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Cavia porcellus	ENSCPOG00000009278	12 retrocopies	retro_cpor_1053, retro_cpor_1215, retro_cpor_1273, retro_cpor_206, retro_cpor_248, retro_cpor_340, retro_cpor_536, retro_cpor_583, retro_cpor_602, retro_cpor_697, retro_cpor_917, retro_cpor_968,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Dipodomys ordii	ENSDORG00000008518	2 retrocopies	retro_dord_370, retro_dord_471,
Echinops telfairi	ENSETEG00000003091	3 retrocopies	retro_etel_1337, retro_etel_1546, retro_etel_248,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Myotis lucifugus	ENSMLUG00000017709	1 retrocopy	retro_mluc_1332,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Mus musculus	ENSMUSG00000060126	8 retrocopies	retro_mmus_1643, retro_mmus_2193, retro_mmus_2354, retro_mmus_2862 , retro_mmus_3264, retro_mmus_3371, retro_mmus_3483, retro_mmus_3496,
Oryctolagus cuniculus	ENSOCUG00000023692	2 retrocopies	retro_ocun_40, retro_ocun_75,
Pteropus vampyrus	ENSPVAG00000003191	15 retrocopies	retro_pvam_1069, retro_pvam_1116, retro_pvam_1142, retro_pvam_1145, retro_pvam_1252, retro_pvam_1266, retro_pvam_1290, retro_pvam_1322, retro_pvam_1387, retro_pvam_242, retro_pvam_369, retro_pvam_547, retro_pvam_585, retro_pvam_721, retro_pvam_801,
Rattus norvegicus	ENSRNOG00000001049	7 retrocopies	retro_rnor_115, retro_rnor_2464, retro_rnor_2706, retro_rnor_411, retro_rnor_886, retro_rnor_908, retro_rnor_958,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,