RetrogeneDB ID: retro_mmus_1605

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:3346717..3347066(-)
• Located in intron of: ENSMUSG00000023800

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tcl1b2
• Ensembl ID: ENSMUSG00000060863
• Aliases: None
• Description: T cell leukemia/lymphoma 1B, 2 [Source:MGI Symbol;Acc:MGI:1351609]

Sequence

>retro_mmus_1605
ATGGCTTATGCAGTTACTCTTCCCCAGCGGTCACTCCCACACATCCTGGTCTTCACAAGACAGGGCATCTATGAAGACGA
GCATCATAAACCGTGGATGGTTGCAAAACTGGAAGCTTGTCCTCATCCGCCATTTTGGGACAGGCTTGGAGTCTGTATAA
CTGTCCACTTGTGGCAGGTGACCAGATACTGTCTAGGACCCTACCTCCTTCCCTCCCGTGAACTTGAACTGTCTACCCAA
GATGTGGAGATTAGACTCCATGAACACACACTGGAGAACAGATGCCATGCTCTGGAGATTAGTGGCACAGTCCCAGGTTG
GTGACACAGAGCAACTGATCCTAATGCTG

Alignment

ORF - retro_mmus_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.12 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAGFYPPRLLPQVLISTGPGFYEDEHHRLWMVAKLETCSHSPYCNKIETCVTVHLWQMTRYPQ-EPAP
          MA.A...P.R.LP..L..T..G.YEDEHH..WMVAKLE.C.H.P.......C.TVHLWQ.TRY....P..
Retrocopy MAYAVTLPQRSLPHILVFTRQGIYEDEHHKPWMVAKLEACPHPPFWDRLGVCITVHLWQVTRYCL>DPTS

Parental  YNPMNYNFLPMTWRLASMNTYRGTDAMHWRLLNHSQVGDTVQLILML
          ..P.N.N.LP..WRL.SMNT...TDAM.WRL...SQVGDT.QLILML
Retrocopy FPPVNLNCLPKMWRLDSMNTHWRTDAMLWRLVAQSQVGDTEQLILML

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	0.26 RPM
SRP007412_cerebellum	0.00 RPM	0.22 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1605 was not detected

EST

No EST(s) were mapped for retro_mmus_1605 retrocopy.

TSS

No TSS is located nearby retro_mmus_1605 retrocopy 5' end.

Lab

retro_mmus_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1605 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000213231	1 retrocopy	retro_hsap_3183,
Gorilla gorilla	ENSGGOG00000013671	1 retrocopy	retro_ggor_1341,
Mus musculus	ENSMUSG00000060863	2 retrocopies	retro_mmus_1150, retro_mmus_1605 ,
Nomascus leucogenys	ENSNLEG00000000495	1 retrocopy	retro_nleu_1660,
Pongo abelii	ENSPPYG00000006118	1 retrocopy	retro_pabe_2642,
Pan troglodytes	ENSPTRG00000006694	1 retrocopy	retro_ptro_2261,