RetrogeneDB ID: retro_mmus_612

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:130412498..130413309(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000040540
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ctdsp2
• Ensembl ID: ENSMUSG00000078429
• Aliases: Ctdsp2, AI586070, D10Ertd73e, OS-4, OS4, SCP2
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:MGI Symbol;Acc:MGI:1098748]

Sequence

>retro_mmus_612
ATGGAACACGGCTCCATCATCACCCAGGCGCGGAGGGAAGACGCCCTGGTGCTCACCAAGCAAGGCCTAGTCTCCAAGTC
CTCGCCTAAGAAGCCCCGTGGCCGCAGCATCTTCAAGGCCCTCTTGTGCTGTTTCCACACACAGCATGTTGTCCAGTCCA
GCTCTTCCACTGAGCTCACACACAAGGAGGAGGCCAACACCATCGCCAAGTCCGATCTGCTCCAGTGTCTCCAGTACCAG
TTTTATCAGATCCCTGGGACCTGCCTGCTCCCCGAGGTGACAGAGCAAGATCAAGGCAGGATCTGCGTGGTCATTGACCT
GGATGAGACCCTTGTGCACAGTTCCTTTAAGCCGATCAACAATGCTGACTTCATAGTGCCTGTAGAGATTGAGGGGACCA
CGCACCAGGTGTATGTGCTCAAGAGGCCTTACGTCGGATGAGTTCCTGAGACGGATGGGGGAGCTCTTCGAATGTGTTCT
CTTCACTGCCAGCTTGGCCAAGTATGCTGACCCTGTGACTGATCTCCTGGACCGGTGCGGGGTGTTCCGGGCCCGCCTGT
TCCGAGAGGCTTGTGTGTTCCACCAGGGCTGCTATGTCAAGGACCTCAGCCGCCTGGGAAGGGACCTGAGGAAAACTGTC
ATCCTGGACAACTCCCCTGCATCTTACATCTTCCACCCAGAAAATGCAGTGCCTGTGCAGTCCTGGTTTGATGACATGGC
AGATACAGAGTTGCTGAACCTGATTCCAGTCTTCGAGGAGCTAAGTGGAACTGATGATGTCTACACCAGCCTTGGGCAGC
TGCGGGCCCCT

Alignment

ORF - retro_mmus_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEHGSIITQARREDALVLTKQGLVSKSSPKKPRGRSIFKALLCCFHTQHVVQSSSSTELTHKEEANTIAK
          MEHGSIITQARREDALVLTKQGLVSKSSPKKPRGRSIFKALLCCFHTQHVVQSSSSTELTHKEEANTIAK
Retrocopy MEHGSIITQARREDALVLTKQGLVSKSSPKKPRGRSIFKALLCCFHTQHVVQSSSSTELTHKEEANTIAK

Parental  SDLLQCLQYQFYQIPGTCLLPEVTEQDQGRICVVIDLDETLVHSSFKPINNADFIVPVEIEGTTHQVYVL
          SDLLQCLQYQFYQIPGTCLLPEVTEQDQGRICVVIDLDETLVHSSFKPINNADFIVPVEIEGTTHQVYVL
Retrocopy SDLLQCLQYQFYQIPGTCLLPEVTEQDQGRICVVIDLDETLVHSSFKPINNADFIVPVEIEGTTHQVYVL

Parental  KRPYV-DEFLRRMGELFECVLFTASLAKYADPVTDLLDRCGVFRARLFREACVFHQGCYVKDLSRLGRDL
          KRPYV.DEFLRRMGELFECVLFTASLAKYADPVTDLLDRCGVFRARLFREACVFHQGCYVKDLSRLGRDL
Retrocopy KRPYV>DEFLRRMGELFECVLFTASLAKYADPVTDLLDRCGVFRARLFREACVFHQGCYVKDLSRLGRDL

Parental  RKTVILDNSPASYIFHPENAVPVQSWFDDMADTELLNLIPVFEELSGTDDVYTSLGQLRAP
          RKTVILDNSPASYIFHPENAVPVQSWFDDMADTELLNLIPVFEELSGTDDVYTSLGQLRAP
Retrocopy RKTVILDNSPASYIFHPENAVPVQSWFDDMADTELLNLIPVFEELSGTDDVYTSLGQLRAP

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	0.14 RPM	75.98 RPM
SRP007412_cerebellum	0.61 RPM	113.98 RPM
SRP007412_heart	0.12 RPM	113.66 RPM
SRP007412_kidney	0.79 RPM	140.71 RPM
SRP007412_liver	0.27 RPM	49.05 RPM
SRP007412_testis	0.69 RPM	28.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_612 was not detected

EST

No EST(s) were mapped for retro_mmus_612 retrocopy.

TSS

No TSS is located nearby retro_mmus_612 retrocopy 5' end.

Lab

retro_mmus_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Mus musculus	ENSMUSG00000026176	2 retrocopies	retro_mmus_1069, retro_mmus_1156,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612 ,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402, retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,