RetrogeneDB ID: retro_ggal_6

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 10:2014384..2015515(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGALG00000001381
• Aliases: ACTG1, actin, cytoplasmic
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSGALG00000028749
• Aliases: None
• Description: Actin, cytoplasmic 2 Actin, cytoplasmic 2, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:Q5ZMQ2]

Sequence

>retro_ggal_6
ATGGCAGATGAGGAAATTGCTGCCCTGGTGGTGGACAATGGCTCTGGTATGTGCAAGGCAGGCTTTGCTGGGGATGATGC
CCCCAGGGCTGTGTTCCCTTCCATTGTGGGACGCCCCCGGCATCAAGGTGTCATGGTGGGTATGGGGCAGAAGGACAGCT
ATGTGGGAGATGAAGCCCAGAGCAAGAGGGGAATCCTCACCCTGAAGTATCCTATTGAGCATGGCATTGTCACCAACTGG
GATGACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGTTGCGTGTTGCTCCAGAGGAGCACCCTGTCCTGCTTAC
TGAGGCCCCGCTGAACCCTAAAGCCAACAGGGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACTCCAGCTATGT
ACGTGGCCATCCAGGCTGTGCTGTCCCTTTATGCCTCTGGTCGCACCACCGGCATCGTCATGGACTCTGGGGATGGTGTC
ACCCACACAGTGCCCATTTACGAGGGCTATGCTCTGCCCCATGCCATCCTGCGTCTGGACTTGGCTGGCCGTGACCTGAC
TGACTACCTCATGAAGATCCTAACAGAGCGAGGTTATAGCTTCACCACCACGGCTGAGAGGGAGATCGTCCGTGATATCA
AGGAAAAGCTGTGCTATGTTGCTCTAGACTTTGAGCAGGAGATGGCAACGGCTGCCTCATCCTCCTCCCTGGAGAAAAGC
TATGAGCTGCCGGATGGGCAGGTGATCACCATTGGGAACGAGCGCTTCCGATGCCCCGAGGCCATCTTCCAACCTTCCTT
CCTGGGCATGGAGTCCTGCGGCATCCACGAGACCACCTTCAACTCCATCATGAAGTGTGATGTGGACATCAGGAAGGACC
TGTATGCCAACACCGTGCTGTCTGGGGGTACCACCATGTACCCTGGCATCGCTGACAGGATGCAGAAGGAGATCACAGCG
CTAGCACCCAGCACCATGAAGATCAAGATCATCGCCCCACCGGAGCGCAAGTATTCTGTCTGGATTGGTGGCTCCATCCT
GGCCTCCCTCTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGATGAGTCTGGCCCCTCCATTGTCCATCGCA
AGTGCTTCTAG

Alignment

ORF - retro_ggal_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.2 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          .EEIAALV.DNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
Retrocopy DEEIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI

Parental  EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
          EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
Retrocopy EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS

Parental  LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
          LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
Retrocopy LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD

Parental  IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNS
          IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEA.FQPSFLGMESCGIHETTFNS
Retrocopy IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEAIFQPSFLGMESCGIHETTFNS

Parental  IMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
          IMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
Retrocopy IMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST

Parental  FQQMWISKQEYDESGPSIVHRKCF
          FQQMWISKQEYDESGPSIVHRKCF
Retrocopy FQQMWISKQEYDESGPSIVHRKCF

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	197.97 RPM	1734.80 RPM
SRP007412_cerebellum	121.58 RPM	1332.59 RPM
SRP007412_heart	45.94 RPM	644.54 RPM
SRP007412_kidney	86.50 RPM	1913.62 RPM
SRP007412_liver	39.61 RPM	2363.64 RPM
SRP007412_testis	313.78 RPM	790.60 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ggal_6 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI390778	2014373	2015000	99.9	621	1	620

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_6 has 1 orthologous retrocopies within neognath group .

Species	RetrogeneDB ID
Meleagris gallopavo	retro_mgal_5

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 143 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Bos taurus	ENSBTAG00000006189	2 retrocopies	retro_btau_286, retro_btau_903,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6 ,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus	ENSMICG00000014863	3 retrocopies	retro_mmur_23, retro_mmur_352, retro_mmur_6,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
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,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,