RetrogeneDB ID: retro_mmus_2394

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:124719139..124719634(+)
• Located in intron of: ENSMUSG00000028902

Retrocopy information

• Ensembl ID: ENSMUSG00000083104
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prelid1
• Ensembl ID: ENSMUSG00000021486
• Aliases: Prelid1, 2610524G07Rik, Preli
• Description: PRELI domain containing 1 [Source:MGI Symbol;Acc:MGI:1913744]

Sequence

>retro_mmus_2394
CAGAGGCTTCTGACCCAGACCAACAAGATGCCACATTGAGCAGAGCGACTGTTTCCTGCCATTGCTGCTCACTCAGCATA
CGTCCTGGAGGACTCTGTTGTGGACCCACAGGATCAGACCATGGCCACCTTCACCTGGAACACCAACCGTGCCTGGCTGG
TGTAGGAGGAGGAGCGATGTGCTTACTGTGTGAGCTCTGACAATAGCTGCTGGGCAGAGATCCATCAGGAAGCCTGGGCC
TCCTCTAGCTTATTTGGCATATCCAGAGCTGTCTAGAAATTTGATCTTGCCTGGTTCACAAGCAATGTGACCAAGACAGT
AAAGGGCTTTGAATATATCCTGGCCAAGCTACAAGGTGAGACCCCCTCCAAAACACTTGTTGAGACAGCCAAAGAGGCCA
AAGAGAAAACAAAGGAGACAGCACTGGCAGCTACAGAGGAGGCCAAAGACCTGACCAACAAGGCTACCACCAAGCAGCAG
CAGCAACAGCTTGTA

Alignment

ORF - retro_mmus_2394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.97 %
• Parental protein coverage: 76.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSG
          .RLLT.TN.MP..AERLFPA..AHS.Y.LEDS.VDPQ.QTM.TFTWN.N.A.L...EERC.YCV.SDNS.
Retrocopy QRLLTQTNKMPH*AERLFPAIAAHSAYVLEDSVVDPQDQTMATFTWNTNRAWLV*EEERCAYCVSSDNSC

Parental  WTEIRREAWVSSSLFGVSRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKET
          W.EI..EAW.SSSLFG.SRAV..F.LA.F.SNVTKT.KGFEYILAKLQGE.PSKTLVETAKEAKEK.KET
Retrocopy WAEIHQEAWASSSLFGISRAV*KFDLAWFTSNVTKTVKGFEYILAKLQGETPSKTLVETAKEAKEKTKET

Parental  ALAATEKAKDLANKAATKQQQRQLV
          ALAATE.AKDL.NKA.TKQQQ.QLV
Retrocopy ALAATEEAKDLTNKATTKQQQQQLV

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	0.16 RPM	36.96 RPM
SRP007412_cerebellum	0.30 RPM	29.44 RPM
SRP007412_heart	0.16 RPM	12.86 RPM
SRP007412_kidney	0.13 RPM	53.88 RPM
SRP007412_liver	0.08 RPM	55.19 RPM
SRP007412_testis	0.05 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_2394 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	4:124719084..124719478

EST

No EST(s) were mapped for retro_mmus_2394 retrocopy.

TSS

No TSS is located nearby retro_mmus_2394 retrocopy 5' end.

Lab

retro_mmus_2394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2394 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2178

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236, retro_mmus_2394 , retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178, retro_rnor_2305, retro_rnor_637, retro_rnor_995,