RetrogeneDB ID: retro_mmus_2326

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:12114283..12115969(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083246
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pabpc4
• Ensembl ID: ENSMUSG00000011257
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]

Sequence

>retro_mmus_2326
ATGAACGCTGCAGCCAGCAGCTACCCCATGGCCTCCTTATACGTGGGCGATTTGCACTCGGACATCACCAAAGCCATGCT
GTATGAAAAGTTCAGCCCTGTGGGGCCTGTGCTGTCCATCCGTGTCTGTCGCGATATGATCACCGGGCGCTCTCTGGGTT
ATGCCTATGTCAACTTCCAGCAGCCAGCCGACGCTGAGAGGGCCTTGGACACCATGAACTTCGACGTCATGAAGGGAAAG
CCAGTCCGCATCATGTGGTCGCAGAGGGATCCCTCTTTGAGAAAGTCTGGGGTGGGAAATGTCTTCATCAAGAACCTGGA
CAAATCCATAGACAACAAGGCACTGTATGACACTTTCTCTGCCTTTGGAAACATCTTGTCCTGTAAGGTGGTCTGTGATG
AGAACGGCTCTAAGGGCTATGCTTTTGTTCACTTCGAGACCCAAGAGGCCGCCGACAAGGTCATCGAGAAGATGAATGGC
ATGCTTCTCAATGACCAGCAAGTGTTTGTGGGTAGATTCAAGTCTCGCAAAGAGCGGGAAGCGGAGCTTGGAGCCAAGGC
CAAGGAATTCACCAATGTTTATATCAAAAACTTCGGAGAAGGGGTGGATGATGGGAATCTGAAAGAGCTCTTCAGCCAGT
TTGGTAAGACCCTAAGTGTCAAGGTGATGAGAGACTCCAGTGGGAAGTCCAAAGGCTTTGGCTTTGTAAGTTACGAGAAA
CACGCGGATGCCAAGAAGGCTGTGGAAGAAATGAATGGAAACGAGATGAGCGGGAAAGCCATATTTGTAGGCCGTGCACA
GAAAAAGGTAGAAAGGCAGGCTGAGCTGAAGCGGAAGTTTGAGCAGCTGAAGCAGGAGAGGATTAGCCGGTACCAGGGGA
TGAATCTCTACATTAAGAACTTGGATGACACCATTGATGATGAGAAATTAAGGAAAGCGTTTTCTCCCTTTGGAACAATC
ACCAGTGCGAAGGTGATGCTGGAAGATGGGAGAAGCAAAGGGTTTGGCTTTGTCTGTTTCCCCTCTCCTGAAGAGGCGAC
CAAAGCTGTCACCGAGATGAATGGACGCATTGTGGGCTCCAAGCCTCTGTATGTCGCCTTGGCCCAGAGGAAGGAAGAAC
GGAAGGCTCACCTGACTAAGCAGTACACGCAGCGTGTGGCGGGGATGAGAGTACTCCCTGCCGGTGCCATCTTAAATCAG
TTCCAGCCTGCAGCTGGTGGCTACTTTGTGCCCGCAGGTGCGCAGGCTCAGGGAAGACCCCCATATTACACGCCTAACCA
GTTAGCACAGATGAGGCCTAATCCACGCTGGCAGCAAGGCGGGAGACCTCAAGGCTTCCAAGGATTGCCAAGTGCCCTGC
GGGGCATGTCTGGGCCTCGTCCAGCTCTTCGACATCTGGCTCCAACTGGTAATGCTCCGGCCTCTCGTGGCCTTCCTACT
ACTGCTCAGAGAGTCGGGTCTGAGTGCCCGGACGGCTTGGCTATGGACTTTGGTGGGGCTGGTGCCGCCCAGCAAGGGCT
GTCTGACAGCTGCCACTCTGGAAGCATCCCTACAGCCACAGTTGCTGCCTCTGCTCCCAGGGCTGTGGCTCCATACAAGT
ATGCCTCCAGTGGCCACAGCCCACACCCTGCCATCCAGCCGCTGCAGGCCCCCCAGCCTGTAGTCCATGTCCAGGGTCAG
GAGCCC

Alignment

ORF - retro_mmus_2326 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 84.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MNAAASSYPMASLYVGDLHSD.T.AMLYEKFSP.GPVLSIRVCRDMIT.RSLGYAYVNFQQPADAERALD
Retrocopy MNAAASSYPMASLYVGDLHSDITKAMLYEKFSPVGPVLSIRVCRDMITGRSLGYAYVNFQQPADAERALD

Parental  TMNFDVMKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVMKGKP.RIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
Retrocopy TMNFDVMKGKPVRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDGNLKEL
          AFVHFETQEAADK.IEKMNGMLLND..VFVGRFKSRKEREAELGAKAKEFTNVYIKNFGE.VDDGNLKEL
Retrocopy AFVHFETQEAADKVIEKMNGMLLNDQQVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEGVDDGNLKEL

Parental  FSQFGKTLSVKVMRDSSGKSKGFGFVSYEKHEDANKAVEEMNGKEMSGKAIFVGRAQKKVERQAELKRKF
          FSQFGKTLSVKVMRDSSGKSKGFGFVSYEKH.DA.KAVEEMNG.EMSGKAIFVGRAQKKVERQAELKRKF
Retrocopy FSQFGKTLSVKVMRDSSGKSKGFGFVSYEKHADAKKAVEEMNGNEMSGKAIFVGRAQKKVERQAELKRKF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRREFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQLKQERISRYQG.NLYIKNLDDTIDDEKLR..FSPFG.ITSAKVMLEDGRSKGFGFVCF.SPEEATKAV
Retrocopy EQLKQERISRYQGMNLYIKNLDDTIDDEKLRKAFSPFGTITSAKVMLEDGRSKGFGFVCFPSPEEATKAV

Parental  TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPASAILNQFQPAAGGYFVPAVPQAQGRP
          TEMNGRIVGSKPLYVALAQRKEERKAHLT.QY.QRVAGMR.LPA.AILNQFQPAAGGYFVPA..QAQGRP
Retrocopy TEMNGRIVGSKPLYVALAQRKEERKAHLTKQYTQRVAGMRVLPAGAILNQFQPAAGGYFVPAGAQAQGRP

Parental  PYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSALR-QSGPRPALRHLAPTGNAPASRGLPTTAQRVGSECP
          PYYTPNQLAQMRPNPRWQQGGRPQGFQG.PSALR..SGPRPALRHLAPTGNAPASRGLPTTAQRVGSECP
Retrocopy PYYTPNQLAQMRPNPRWQQGGRPQGFQGLPSALRGMSGPRPALRHLAPTGNAPASRGLPTTAQRVGSECP

Parental  DRLAMDFGGAGAAQQGLTDSCQSGGVPTA-VPNLAPRA-AVAAAAPRAVAPYKYASSVRSPHPAIQPLQA
          D.LAMDFGGAGAAQQGL.DSC.SG..PTA.V...APRA.A....A.....P.........P.P.....Q.
Retrocopy DGLAMDFGGAGAAQQGLSDSCHSGSIPTATVAASAPRAVAPYKYASSGHSPHPAIQPLQAPQPVVH-VQG

Parental  PQP
          ..P
Retrocopy QEP

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	0.35 RPM	13.06 RPM
SRP007412_cerebellum	0.09 RPM	9.60 RPM
SRP007412_heart	0.44 RPM	120.01 RPM
SRP007412_kidney	0.19 RPM	35.50 RPM
SRP007412_liver	0.05 RPM	16.19 RPM
SRP007412_testis	1.37 RPM	3.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2326 was not detected

EST

4 EST(s) were mapped to retro_mmus_2326 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA681546	12114950	12115421	97.2	451	13	432
AI608590	12114939	12115346	99.3	400	3	395
CN718034	12114328	12114960	99.9	631	1	630
CN724964	12114328	12114877	99.5	546	3	543

TSS

No TSS is located nearby retro_mmus_2326 retrocopy 5' end.

Lab

retro_mmus_2326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2326 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326 , retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,