RetrogeneDB ID: retro_mmus_638

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:42330788..42331263(-)
• Located in intron of: ENSMUSG00000038302

Retrocopy information

• Ensembl ID: ENSMUSG00000081873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snrpc
• Ensembl ID: ENSMUSG00000024217
• Aliases: Snrpc, Snrp1c, U1-C, U1C
• Description: U1 small nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:109489]

Sequence

>retro_mmus_638
ATGCCCAAGTTTTATTGTGACTACTGTGAAACTTATCTTACCCACGACTCTCCATCTGTGAGGAAGACACACTGCAGTGG
TTGGAAACCCAAAGAGAATGTGACAGACTATCACCAGAAAGGGATGGAAGATCAGGCCCAGAGCCTAATTGACAAGACAA
CGGCTGCATTTCAACAAGGGAAGATCCCTCCGCTCCGTTCTCTGCTCCTCCACCTGCAGGGGCCATGATTCCACTGCTCC
CCAGTCTCCTGAGTCCTCCTTGGCCTGGCATGATGCCTGCATCCCACATGGGAGACCCTCTCATGATGCCAGTGATGGGC
CCCCTCCTCCTGGGATGATGCCTGTGGGACCTGCTCCTGGGATGCAACCACCCATGGGAGGCCACATGCCCATGATGCCC
TGGCTTCCCATGATGAGACCTCCCGCCTGTCCTATGATGGTACCCACACAGCCTGGCATGACTCAGCCAGACAGA

Alignment

ORF - retro_mmus_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPP-APFSA
          MPKFYCDYC.TYLTHDSPSVRKTHCSG.K.KENV.DY.QK.ME.QAQSLIDKTTAAFQQGKIPP.APFSA
Retrocopy MPKFYCDYCETYLTHDSPSVRKTHCSGWKPKENVTDYHQKGMEDQAQSLIDKTTAAFQQGKIPP<APFSA

Parental  PPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMM-GPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPM
          PPPAGAMIP..PSL..PP.PGMMPA.HMG.P.MMP.M.GPPPPGMMPVGPAPGM.PPMGGHMPMMP..PM
Retrocopy PPPAGAMIPLLPSLLSPPWPGMMPASHMGDPLMMPVM<GPPPPGMMPVGPAPGMQPPMGGHMPMMPWLPM

Parental  MRPPARPMMVPTRPGMTRPDR
          MRPPA.PMMVPT.PGMT.PDR
Retrocopy MRPPACPMMVPTQPGMTQPDR

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	0.02 RPM	9.32 RPM
SRP007412_cerebellum	0.09 RPM	10.86 RPM
SRP007412_heart	0.09 RPM	7.94 RPM
SRP007412_kidney	0.06 RPM	11.57 RPM
SRP007412_liver	0.03 RPM	6.69 RPM
SRP007412_testis	0.00 RPM	51.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_638 was not detected

EST

No EST(s) were mapped for retro_mmus_638 retrocopy.

TSS

No TSS is located nearby retro_mmus_638 retrocopy 5' end.

Lab

retro_mmus_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Mus musculus	ENSMUSG00000024217	21 retrocopies	retro_mmus_1079, retro_mmus_1084, retro_mmus_1231, retro_mmus_1313, retro_mmus_1374, retro_mmus_1400, retro_mmus_1515, retro_mmus_1649, retro_mmus_1673, retro_mmus_1781, retro_mmus_1876, retro_mmus_2087, retro_mmus_2211, retro_mmus_2506, retro_mmus_2973, retro_mmus_3089, retro_mmus_3366, retro_mmus_431, retro_mmus_531, retro_mmus_566, retro_mmus_638 ,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii	ENSPPYG00000017272	4 retrocopies	retro_pabe_1271, retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Rattus norvegicus	ENSRNOG00000000493	30 retrocopies	retro_rnor_1027, retro_rnor_1079, retro_rnor_1100, retro_rnor_1196, retro_rnor_1219, retro_rnor_1421, retro_rnor_1628, retro_rnor_1637, retro_rnor_1701, retro_rnor_1761, retro_rnor_2259, retro_rnor_2261, retro_rnor_2385, retro_rnor_2480, retro_rnor_2663, retro_rnor_2875, retro_rnor_2893, retro_rnor_445, retro_rnor_483, retro_rnor_495, retro_rnor_502, retro_rnor_630, retro_rnor_705, retro_rnor_706, retro_rnor_707, retro_rnor_730, retro_rnor_747, retro_rnor_778, retro_rnor_802, retro_rnor_889,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,
Sus scrofa	ENSSSCG00000001531	1 retrocopy	retro_sscr_709,