RetrogeneDB ID: retro_btau_336

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:22434636..22435580(+)
• Located in intron of: ENSBTAG00000000432

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.64559
• Ensembl ID: ENSBTAG00000013631
• Aliases: None
• Description: Glutamine synthetase [Source:UniProtKB/Swiss-Prot;Acc:P15103]

Sequence

>retro_btau_336
TGGAATTTTGATGGCTCTAGTTACTTTTCAGTCTGAAGACACCAACAGTGATGTGTATCTTGTCTCTGCTGCCATGTTTC
GGGACCCTTTCCACAAGGACCCCCAACAAGCTGGTGTTCTGTGAAGTCTTCAAGTACAACCAAAAGCCTGCTGACACCAA
TTTAAGGCACACTTATAAATGGATAATGGACATGGTCAGCAACCAGTGCCTATGGTTTGGAATGGAGCACGAATATACCC
TCATGGGCACAGATGGGCACCCCTTTGGTTGGCCTTCCAACGGCTTTCCTGGGCCCTAACATCCATACTACTGTGGTGTG
GGAGCGGACAAGGCTTACCGCAGGGATATTGTGGAGATTCACCACCCAGCCTGCTTGCAGGCAGGCATCAAGATCCAGGG
TAGGAACGCCGAGGTCATGCCTGTGCAGTGGGAATTCCAGATAGGACCCTGTGAAGGAGTCAACATGGGAGATCATCTGT
GGGTGGCCCATTTCATCTTGCATCATGTGTGCGAAGACTTCGGAGTGATCACCACCTTTGAGCCTAAGCCCATTCTTGGG
AACGGGAATGGTGCCGGCTGCCACCCCAACTTTAGCACCAAGGCCATGCGAGAGGAGAATGGTCTGAAGTACACTGAGGA
GGGCACTGAGAAACTAAGCAAGGGGCAGCAGTGCCACATCCGAGCCTATGAACCCAAGGGGGCCGTGGACAACGCCCGGC
GCCTAACTGGATTCCACGAAACCTCCAACATCAAGGACTTCTCTGCCGGTGGGGCCAACCTTGGCGCCAGCATCCACATC
CCTCGGACTGTTTGCCAGGAGAAGAAAGGCTACTTTGAAGACCGTCGCCCTTCTGCCAACTGTGACCCCTCTGCCATGAT
GGAAGCCCTCATCCGCACATGTCTTCTGAACGAAATGGGCGATGAGCTCTTCCAGTACAAGAAC

Alignment

ORF - retro_btau_336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 84.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WNFDGSS-TFQSEGSNSDMYLVPAAMFRDPFRKDP-NKLVFCEVFKYNRKPAETNLRHTCKRIMDMVSNQ
          WNFDGSS.TFQSE..NSD.YLV.AAMFRDPF.KDP.NKLVFCEVFKYN.KPA.TNLRHT.K.IMDMVSNQ
Retrocopy WNFDGSS>TFQSEDTNSDVYLVSAAMFRDPFHKDP>NKLVFCEVFKYNQKPADTNLRHTYKWIMDMVSNQ

Parental  RPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGADKAYGRDIVEAHYRACLYAGIKIGGTNAEV
          ..WFGME.EYTLMGTDGHPFGWPSNGFPGP..PYYCGVGADKAY.RDIVE.H..ACL.AGIKI.G.NAEV
Retrocopy CLWFGMEHEYTLMGTDGHPFGWPSNGFPGP*HPYYCGVGADKAYRRDIVEIHHPACLQAGIKIQGRNAEV

Parental  MPAQWEFQIGPCEGIDMGDHLWVARFILHRVCEDFGVIATFDPKPIPGNWNGAGCHTNFSTKAMREENGL
          MP.QWEFQIGPCEG..MGDHLWVA.FILH.VCEDFGVI.TF.PKPI.GN.NGAGCH.NFSTKAMREENGL
Retrocopy MPVQWEFQIGPCEGVNMGDHLWVAHFILHHVCEDFGVITTFEPKPILGNGNGAGCHPNFSTKAMREENGL

Parental  KYIEEAIEKLSKRHQYHIRAYDPKGGLDNARRLTGFHETSNINDFSAGVANRGASIRIPRTVGQEKKGYF
          KY.EE..EKLSK..Q.HIRAY.PKG..DNARRLTGFHETSNI.DFSAG.AN.GASI.IPRTV.QEKKGYF
Retrocopy KYTEEGTEKLSKGQQCHIRAYEPKGAVDNARRLTGFHETSNIKDFSAGGANLGASIHIPRTVCQEKKGYF

Parental  EDRRPSANCDPFAVTEALIRTCLLNETGDEPFQYKN
          EDRRPSANCDP.A..EALIRTCLLNE.GDE.FQYKN
Retrocopy EDRRPSANCDPSAMMEALIRTCLLNEMGDELFQYKN

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	97.19 RPM
ERP005899_muscle	0.00 RPM	105.05 RPM
SRP017611_brain	0.00 RPM	2225.86 RPM
SRP017611_kidney	0.00 RPM	357.59 RPM
SRP017611_liver	0.00 RPM	226.53 RPM
SRP030211_testis	0.06 RPM	456.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_336 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013631	4 retrocopies	retro_btau_1050, retro_btau_1474, retro_btau_336 , retro_btau_824,
Canis familiaris	ENSCAFG00000013102	2 retrocopies	retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus	ENSCJAG00000004654	1 retrocopy	retro_cjac_2837,
Dasypus novemcinctus	ENSDNOG00000013948	4 retrocopies	retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus	ENSECAG00000015865	1 retrocopy	retro_ecab_979,
Echinops telfairi	ENSETEG00000008329	3 retrocopies	retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus	ENSFCAG00000010551	1 retrocopy	retro_fcat_1811,
Homo sapiens	ENSG00000135821	4 retrocopies	retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla	ENSGGOG00000024712	3 retrocopies	retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana	ENSLAFG00000000700	1 retrocopy	retro_lafr_196,
Macropus eugenii	ENSMEUG00000001774	6 retrocopies	retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta	ENSMMUG00000022884	2 retrocopies	retro_mmul_2047, retro_mmul_954,
Monodelphis domestica	ENSMODG00000006787	4 retrocopies	retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus	ENSMUSG00000026473	3 retrocopies	retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys	ENSNLEG00000018007	3 retrocopies	retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii	ENSPPYG00000000440	1 retrocopy	retro_pabe_2698,
Pan troglodytes	ENSPTRG00000001751	4 retrocopies	retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii	ENSSHAG00000000116	1 retrocopy	retro_shar_553,
Sus scrofa	ENSSSCG00000015545	1 retrocopy	retro_sscr_726,
Ictidomys tridecemlineatus	ENSSTOG00000014529	2 retrocopies	retro_itri_1083, retro_itri_743,
Tupaia belangeri	ENSTBEG00000003522	3 retrocopies	retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta	ENSTSYG00000002066	1 retrocopy	retro_tsyr_385,
Tursiops truncatus	ENSTTRG00000010781	1 retrocopy	retro_ttru_543,
Drosophila melanogaster	FBgn0001145	1 retrocopy	retro_dmel_44,