RetrogeneDB ID: retro_btau_562

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:51233304..51233801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSBTAG00000008731
• Aliases: PRDX3, MTAP
• Description: Thioredoxin-dependent peroxide reductase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P35705]

Sequence

>retro_btau_562
AAGGGGAAATATTTGGTGCTCTTCGTCTATCCTTTGAATTTCACTTTTGCGAACAGAAATTTCACAATTGCTTTCAGTGA
CAAAGCCAGTGAATTTCATGATGTGAACTGTGCACTTGCTGCAGTGTTAATGGGTTCCCACTTCAGCCACCTGGCCTAGA
TGAACACACAGAGGAAGAATGCTGGTTTGGGCCACATGAACATTAAGCTCTTGTCAGATTTGACTTAACAGCTCCCCCGA
CACTACAGTGTCCAGTGAGAAGGTTCTGATCCTTCACTATGAGTTCTTTTCATAATTGATGCCAATGGAGTCATCAAGTA
TTTGAGTATCAATGATCTCCCAGTGGGCTGAAGCATGGAAGGAACCCTCTGCTTGGTGAAGGCATTTCAGTTTGTGGAAA
CCAATGCAGAAGTCTGCCCAGCCAATAGGACATCAGCTTCTCCTGTAATTAAGCCCCATCCAACTGCTTCCAAAAAAACT
TTGAGAAGGTAAATCAG

Alignment

ORF - retro_btau_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.06 %
• Parental protein coverage: 64.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGKYLVLFFYPLDFTFVCPTEIIAFSDKASEFHDVNCEVVAVSVDSHFSHLAWINTPRKNGGLGHMNIAL
          KGKYLVLF.YPL.FTF......IAFSDKASEFHDVNC...AV...SHFSHLA..NT.RKN.GLGHMNI.L
Retrocopy KGKYLVLFVYPLNFTFANRNFTIAFSDKASEFHDVNCALAAVLMGSHFSHLA*MNTQRKNAGLGHMNIKL

Parental  LSDLTKQISRDYGVLLEGPGLALRGLFIIDPNGVIKHLSVNDLPVGRSVEETLRLVKAFQFVEAHGEVCP
          LSDLT.Q..R.Y.V..EG....L..LFIID.NGVIK.LS.NDLPVG.S.E.TL.LVKAFQFVE...EVCP
Retrocopy LSDLT*QLPRHYSVQ*EGSDPSL*VLFIIDANGVIKYLSINDLPVG*SMEGTLCLVKAFQFVETNAEVCP

Parental  ANWTPESPTIKPHPTASR-EYFEKVNQ
          AN.T..SP.IKPHPTAS....FEKVNQ
Retrocopy ANRTSASPVIKPHPTASK<KNFEKVNQ

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	345.99 RPM
ERP005899_muscle	0.00 RPM	67.62 RPM
SRP017611_brain	0.00 RPM	50.61 RPM
SRP017611_kidney	0.00 RPM	180.01 RPM
SRP017611_liver	0.00 RPM	172.54 RPM
SRP030211_testis	0.00 RPM	17.20 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_562 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003642	2 retrocopies	retro_btau_1299, retro_btau_1446,
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562 ,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,