RetrogeneDB ID: retro_mmus_1613

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:8565892..8566945(-)
• Located in intron of: ENSMUSG00000023868

Retrocopy information

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

Parental gene information

• Parental gene symbol: Actb
• Ensembl ID: ENSMUSG00000029580
• Aliases: Actb, Actx, E430023M04Rik, beta-actin
• Description: actin, beta [Source:MGI Symbol;Acc:MGI:87904]

Sequence

>retro_mmus_1613
ATAAATGATGATATCACTGTGCTAGTCAACGTTGACAATGGCTCTGGCTTGTGCAAAGCTGCCTTTGCGAGCGACGATGC
TTCCCCAGGCCATCTTCCCCTCCATCGTGGGCCTCCCTAGGCACCAGGGTATGATGGTGGGTATGGGTCAGAGGGACTCT
TATGTGGGCGACGAGGCCCAAAGCAAGAGAGGCTTCCTGACCCTGAAGTACCCCATTGAACATGGCATTGTCACCAACTG
GGACAATATAAAGAAGGTCTGGCACCATACCTTTTACAATGAGCTGCGTGTGGCCCCTGAGGAGTACCCTGTACTGCTCA
CTGAAGGCCCCCTGAACCCTAAGGCCAACCGTGAAAAGATGACCCAGATCATGTTTGAGACCTTCAACATCCCAGCCATG
TACAACGCCATCCAGGCTGTGTTGTCCCTATATGCATCTGGTTGTACCACTGGTATTTTGATGGACTTCAGAGATGGGTT
ACCCACATTATGCCCATCTACGAGGGCTATGCCATGCTGTGTCTGGACCTGGCTGGCCGGGACCTGACAGTGTACCTCAT
GAAGATCCTGACCCAGCGTGGCTACAGCTTCACCAACATGGCTGAGAGGGAAATCATGCGTGACAAAGAGAAGCTGTGCT
ATGTTGCCCTAGACTTTGAGCAGGAGATGGCCACTGCCGCATTCTCTTCTTCCCTGGAGAAGAGCTATAAGCTGCCTGAC
AGACAGGTCATCACTATTGGCAATAAGCGGTTCCAATGCCCTGGGGCTCTTTTCCAGCCTTCCTTCTTGAGTATGGAATC
CTGTGGCATCCATGAAACTACATTCAATTCCATCATGAAGTATGACATTGACATTTGTAAAGACTTCTATGCCAACACAG
TGCTATCTGGTAGCACCACTATGCACCCAAACATTGCTGACAGGATGCAGAAGGAGATCACTGCTCTAGATCCTAGCACC
AAGAAGACCAAGATCATTGCTCCTCCTAAGCTCAGGTACTCTGTGTAGATCAGTGGCTCCATCCTGGCCTCCACCTTCCA
GCAGACGTGGATC

Alignment

ORF - retro_mmus_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.39 %
• Parental protein coverage: 95.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALV-VDNGSGMCKAGFAGDDA-PRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
          ..DDI..LV.VDNGSG.CKA.FA.DDA.P.A.FPSIVG.PRHQG.MVGMGQ.DSYVGDEAQSKRG.LTLK
Retrocopy INDDITVLVNVDNGSGLCKAAFASDDA>PQAIFPSIVGLPRHQGMMVGMGQRDSYVGDEAQSKRGFLTLK

Parental  YPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQA
          YPIEHGIVTNWD...K.WHHTFYNELRVAPEE.PVLLTE.PLNPKANREKMTQIMFETFN.PAMY.AIQA
Retrocopy YPIEHGIVTNWDNIKKVWHHTFYNELRVAPEEYPVLLTEGPLNPKANREKMTQIMFETFNIPAMYNAIQA

Parental  VLSLYASGRTTGIVMDSGDG-VTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAERE
          VLSLYASG.TTGI.MD..DG.VTH..PIYEGYA.....L.LDLAGRDLT.YLMKILT.RGYSFT..AERE
Retrocopy VLSLYASGCTTGILMDFRDG<VTHIMPIYEGYAM----LCLDLAGRDLTVYLMKILTQRGYSFTNMAERE

Parental  IVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHET
          I.RD.KEKLCYVALDFEQEMATAA.SSSLEKSY.LPD.QVITIGN.RF.CP.ALFQPSFL.MESCGIHET
Retrocopy IMRD-KEKLCYVALDFEQEMATAAFSSSLEKSYKLPDRQVITIGNKRFQCPGALFQPSFLSMESCGIHET

Parental  TFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILA
          TFNSIMK.D.DI.KD.YANTVLSG.TTM.P.IADRMQKEITAL.PST.K.KIIAPP...YSV.I.GSILA
Retrocopy TFNSIMKYDIDICKDFYANTVLSGSTTMHPNIADRMQKEITALDPSTKKTKIIAPPKLRYSV*ISGSILA

Parental  SLSTFQQMWI
          ..STFQQ.WI
Retrocopy --STFQQTWI

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	0.21 RPM	922.02 RPM
SRP007412_cerebellum	0.48 RPM	706.77 RPM
SRP007412_heart	0.16 RPM	464.18 RPM
SRP007412_kidney	0.25 RPM	679.61 RPM
SRP007412_liver	0.03 RPM	437.32 RPM
SRP007412_testis	0.14 RPM	567.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1613 was not detected

EST

No EST(s) were mapped for retro_mmus_1613 retrocopy.

TSS

No TSS is located nearby retro_mmus_1613 retrocopy 5' end.

Lab

retro_mmus_1613 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1613 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000025228	1 retrocopy	retro_mmus_2686,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613 , retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,