RetrogeneDB ID: retro_btau_903

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:21814401..21815523(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046468
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSBTAG00000006189
• Aliases: None
• Description: Actin, cytoplasmic 2 Actin, cytoplasmic 2, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:P63258]

Sequence

>retro_btau_903
GATGACGAGCTGTCTGCCTTGGTGGTGGATAATGGGTCAGGGATGTGCAAGGCAGGCTTTGGCGGTGACGATGCCCCCAG
GGCTGTGTTCCCCTCTATGGTGGGGCGTCCCCGGCACCAGGGGGTCATGGTAGGCATGGGCCAGAAGGACTGCTACGTGG
GGGATGAGGCCCAGAGCAAGAGAGGCATCCTGACCCTGAAGTACCCCATTGAGCATGGAGTGGTCACCAACTGGGATGAC
ATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTCCGCGTGGCTCCAGATGAGCATCCCATCCTCCTCACTGAGGC
ACCCCTCAACCCCAAGATCAACCGGGAGAAGATGACTCAGATCATGTTTGAGGCTTTCAACACACCTGCCATGTATGTGG
CCATCCAGGCCGTGCTGTCCCTCTACGCCTCAGGCCGGACCACCGGCATCGTGATGGATTCTGGGGATGGGGTCACTCAC
ACTGTACCCATCTATGAAGGCTATGCCTTGCCTCATGCCATTCTACGTCTGGACCTGGCCGGCAGAGACCTGACCGATTA
CCTCATGAAGATCCTGACAGAACGAGGCTACAGCTTCACCACCACGGCTGAGCGGGAGATTGTTCGTGACGTCAAAGAGA
AGCTGTGTTATGTGGCCCTAGACTTTGAGCAAGAGATGGTCAGCACTGCAGCATCCTCCTCCCTGGAGAGAAGCTACGAG
CTTCCCGACGGGCAGGTGATCACTATTGGGAATGAGCGCTTTCGATGTCCAGAAGCCATTTTCCAGCCTTCCTTTCTGGG
CATTGAGTCCAGTGGAATCCACGAGACAACCTTCAACTCTATTATGAAGTGCGATGTGGATATTCGCAAGGATCTGTACG
CCAACACCGTGCTGTCTGGAGGCAGCACTATGTACCCTGGCATTGCTGAACGGATGCAGAAGGAAATTGTAGCCTTGGCA
CCCAGCACCATGAAAATCAAGATCATTGCTCCCCCAGAACGGAAGTACTCCGTTTGGATTGGGGGCTCCATTCTGGCCAG
CCTGTCCACGTTCCAGCAAATGTGGATCAGTAAGCAGGAGTATGATGAGGCTGGGCCTCCCATTGTCCACAGGAAGTGTT
TC

Alignment

ORF - retro_btau_903 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          ..E..ALV.DNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYPI
Retrocopy DDELSALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYPI

Parental  EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
          EHG.VTNWDDMEKIWHHTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVLS
Retrocopy EHGVVTNWDDMEKIWHHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVLS

Parental  LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
          LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
Retrocopy LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD

Parental  IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNS
          .KEKLCYVALDFEQEM...A.SSSLE.SYELPDGQVITIGNERFRCPEA.FQPSFLG.ES.GIHETTFNS
Retrocopy VKEKLCYVALDFEQEMVSTAASSSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGIESSGIHETTFNS

Parental  IMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
          IMKCDVDIRKDLYANTVLSGG.TMYPGIA.RMQKEI.ALAPSTMKIKIIAPPERKYSVWIGGSILASLST
Retrocopy IMKCDVDIRKDLYANTVLSGGSTMYPGIAERMQKEIVALAPSTMKIKIIAPPERKYSVWIGGSILASLST

Parental  FQQMWISKQEYDESGPSIVHRKCF
          FQQMWISKQEYDE.GP.IVHRKCF
Retrocopy FQQMWISKQEYDEAGPPIVHRKCF

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
ERP005899_liver	0.00 RPM	302.08 RPM
ERP005899_muscle	0.00 RPM	2089.81 RPM
SRP017611_brain	0.00 RPM	787.60 RPM
SRP017611_kidney	0.00 RPM	986.34 RPM
SRP017611_liver	0.00 RPM	119.91 RPM
SRP030211_testis	0.01 RPM	527.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_903 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_903 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_38
Pan troglodytes	retro_ptro_53
Gorilla gorilla	retro_ggor_1297
Pongo abelii	retro_pabe_86
Callithrix jacchus	retro_cjac_243
Mus musculus	retro_mmus_283
Rattus norvegicus	retro_rnor_351
Oryctolagus cuniculus	retro_ocun_38
Canis familiaris	retro_cfam_934
Equus caballus	retro_ecab_98

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
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,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
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,
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,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,