RetrogeneDB ID: retro_btau_286

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:157502178..157502783(+)
• Located in intron of: None

Retrocopy information

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

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_286
GCCTCTGGCCACACCACGTGTACTGTCCTGGACTCTGAGGAGGGGGTCACCCACACTGTGCCCATCCACCAGGAGTTATG
CCACTCTCCCTGCCATCCCCATCATCCATCTGGACCTCTCTTTCTGGGACCTGACTGACCACCTCGTGAAGATGTTCCCG
GAGTGAGACCACAGCTTCACCATCACTGCCCAGTGGGAAATCCTGTGTGAATCAAGGAGCAACTGTGCCAGGGTCCCCGG
AACTGGAGCAGGAGGTGGCCACTTCTGTGTCCTCCTCCTCCCCAGAGAAGAGCTGTGAGCTGCCAGACCTTCAGGTGACC
AGCATCTTCAACACATGGTTCTGGGATCCAGAGGCACTTTCCCAGCCCTCCTCCTGGGTATGAAGTCCTGTGGCAGCCAC
ACACCCACATTTAGCTCCATCCCACAGGATGATGTCCACATGTAGAAGGACTGTATGCCCACAGGGTGCTGTCTGGGGGA
CCAGCATGTACCCCATGTCACCGGCAGGATGCAGAGAGAGGTCGTGGGCACTGGCGACCCGCAGGACCAGGACTGAGCTC
AAGGTCAGGGGTCCTCCTGGACACACGTACTCGGTGAGGGTGGGG

Alignment

ORF - retro_btau_286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.61 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  ASGRTTGIVMDSGDGVTHTVPIYE-GYALPHAI--LRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          ASG.TT..V.DS..GVTHTVPI....YA...AI....LDL...DLTD.L.K...E...SFT.TA..EI..
Retrocopy ASGHTTCTVLDSEEGVTHTVPIHQ>SYATLPAIPIIHLDLSFWDLTDHLVKMFPE*DHSFTITAQWEILC

Parental  D-IKEKLCYVALDF-EQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPS-FLGMESCGIHET
          ..IKE.LC.......EQE.AT..SSSS.EKS.ELPD.QV..I.N..F..PEAL.QPS..LGM.SCG.H..
Retrocopy E<IKEQLCQGPRNW<EQEVATSVSSSSPEKSCELPDLQVTSIFNTWFWDPEALSQPS<LLGMKSCGSHTP

Parental  TFNSIMKCDVDIRKD-LYANTVLSG-GTTMY-PGIADRMQKEIT-ALAP--STMKIKIIAPPERKYSVWI
          TF.SI...DV...KD.LYA..VLSG.GT.MY.P....RMQ.E...ALA........K...PP...YSV..
Retrocopy TFSSIPQDDVHM*KD<LYAHRVLSG<GTSMY<PHVTGRMQREVV>ALATRRTRTELKVRGPPGHTYSVRV

Parental  G
          G
Retrocopy G

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	0.03 RPM	527.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_286 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_286 has 0 orthologous retrocopies within eutheria group .

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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,