RetrogeneDB ID: retro_ggal_4

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 21:1261035..1262148(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGALG00000001078
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gga-mir-3533
• Ensembl ID: ENSGALG00000009621
• Aliases: ACTB, Bact, actin
• Description: gga-mir-3533 [Source:miRBase;Acc:MI0015386]

Sequence

>retro_ggal_4
GATGTCCCAGCTGTAATCTTTGACAACGGGTCTGGATTGTGCAAGGCGGGGATCGCAGGGGACGGTGGCCCAAGGTCAGT
TATCACATCGATCGTCGGTCGCTCAAGAGTCAAATCTGCAATGCTGGGAGCTGGGATGAAAGAGTACTACGTAGGAGAAG
AAGCTCAGTCCAAAAGAGGGATCCTGACTTTGAATTATCCCATTGACCATGGCATCGTTACATCCTGGGATGACATGGAA
AGGATCTGGAGACACGTCTATGACTACGAGCTGAGAGTGAAAGCCAGCGAAAGACCCGTGCTGCTCACAGAACCCCCCCT
CAACCCCCTGCAGAACCGGGAAAGAATGACTGAGATCATGTTTGAGGGCTTCATGGTGCCCGCCATGTACGTGGCAGTCC
AGGCTGCGTTGGCCCTCTACGCGTCTGCCCGCACCACCGGCATAGTTCTGGACAGCGGGGATGGCGTCACCCACACCGTC
CCCATTTACGAGGGGTACTGCCTGCCCCATGCCGTGTCCAGGCTGGATATCGCTGGCCGGGATATCACTGAGTATTTTAT
GAGGCTCCTTTTGGAGAGCGGATACTCTTTCGTTAGCACCGCTGAAAGGGAAATTGTGAAAGATATCAAAGAGAAGCTGT
GCTATGTGGCTCTAGACCCCACTCTGGAAATGAAAGCAAGTCCAGAAGAAATCATGAAAGAATACAGATTACCTGACAGC
AACATCATTCAGATAGGCAGCCAGCTCTTTCGTGCACCAGAGACCCTTTTTGTACCTGCCAACGTTGGCATTGAAGCAGC
TGGTGTGCACAAAATGCTCTTCAACAGCGTCACAAAGTGCGACATCGATGTGCGCAGGGATCTGTATGGCAACGTGCTGC
TCTCGGGAGGCTCCACGCTCTTCCCTGGCCTGGAGGAGCGCATCCTGAAGGAGATGCACCTGCAGGTGCCTGTGGGGATG
CTCGTGAAAATCATTGCCCCTCCCGAGAGGAAGTACAGCGTGTGGGTCGGGGCCTCCGTCCTCTCCTGCCTGACCTCCTT
CAAATCAATGTGGATCACCGTGAGGGACTACGGGGATTTTGGGGCAGCTGTCGTCCACCGGAAATGCTGTTAA

Alignment

ORF - retro_ggal_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 98.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEH
          D..A...DNGSG.CKAG.AGD..PR.V..SIVGR.R....M.G.G.K..YVG.EAQSKRGILTL.YPI.H
Retrocopy DVPAVIFDNGSGLCKAGIAGDGGPRSVITSIVGRSRVKSAMLGAGMKEYYVGEEAQSKRGILTLNYPIDH

Parental  GIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLY
          GIVT.WDDME.IW.H....ELRV...E.PVLLTE.PLNP..NRE.MT.IMFE.F..PAMYVA.QA.L.LY
Retrocopy GIVTSWDDMERIWRHVYDYELRVKASERPVLLTEPPLNPLQNRERMTEIMFEGFMVPAMYVAVQAALALY

Parental  ASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIK
          AS.RTTGIV.DSGDGVTHTVPIYEGY.LPHA..RLD.AGRD.T.Y.M..L.E.GYSF..TAEREIV.DIK
Retrocopy ASARTTGIVLDSGDGVTHTVPIYEGYCLPHAVSRLDIAGRDITEYFMRLLLESGYSFVSTAEREIVKDIK

Parental  EKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIM
          EKLCYVALD...EM...AS.....K.Y.LPD...I.IG...FR.PE.LF.P...G.E..G.H...FNS..
Retrocopy EKLCYVALDPTLEM--KASPEEIMKEYRLPDSNIIQIGSQLFRAPETLFVPANVGIEAAGVHKMLFNSVT

Parental  KCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQ
          KCD.D.R.DLY.N..LSGG.T..PG...R..KE.....P..M..KIIAPPERKYSVW.G.S.L..L..F.
Retrocopy KCDIDVRRDLYGNVLLSGGSTLFPGLEERILKEMHLQVPVGMLVKIIAPPERKYSVWVGASVLSCLTSFK

Parental  QMWISKQEYDESGPSIVHRKC
          .MWI....Y...G...VHRKC
Retrocopy SMWITVRDYGDFGAAVVHRKC

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	0.00 RPM	1212.09 RPM
SRP007412_cerebellum	0.00 RPM	1107.92 RPM
SRP007412_heart	0.05 RPM	600.17 RPM
SRP007412_kidney	0.00 RPM	1468.61 RPM
SRP007412_liver	0.00 RPM	2239.38 RPM
SRP007412_testis	182.92 RPM	603.54 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_4 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_4 has 1 orthologous retrocopies within neognath group .

Species	RetrogeneDB ID
Meleagris gallopavo	retro_mgal_6

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 89 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 ,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
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	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
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,