RetrogeneDB ID: retro_btau_1465

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:90636330..90637194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000027534
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5C3
• Ensembl ID: ENSBTAG00000016709
• Aliases: None
• Description: cytosolic 5'-nucleotidase 3 [Source:RefSeq peptide;Acc:NP_001032686]

Sequence

>retro_btau_1465
ATCGAAATGATGCCGGAAATCCAGAAAAATTCAGTTCACATCAAGAACCCTACAAGAATAGAAGAAATTATCTGTGGTCT
TATCAAAGGAGGAGCTGCTAAACTTCAGATAATAACAGACTTTGATATGACACTGAGTCAATTTTCCTACAAAGGAAAAA
GATGCCCATCATGTCATAATGTCATTGACAACTATAAGCTAATCACAGATGAATGTCGAGAAAAGTTACTGCAACTAAAG
GAAAAATATTATGCTATTGAAGTTGATCCTGTTCTTACTATAGAAGAGAAGTACCCTTATATAGTAGAATGGTATACTAA
ATCACATAGTTTGCTTGTTGAACAGGCTTTACCGAAAGCCAAACTTAAAGAAATTGTGGAAGAATCTGACATTATGCTCA
AGGAAGGATATGAGAATTTCTTTGATAAGCTGCAACAATACAGTATTCCTGTGTTCATATTTTCGGCTGGTATCGGTGAT
GTGCTGGAGGAAGTTATCCGTCAAGCTGGTGTATATTACCCAAATGTCAAAGTGGTGTCCAACTTCATGGATTTTGATGA
CAATGGGCTGCTCAAAGGATTTAAAGGAGAACTAATTCATGTGTTTAACAAACATGATGGTTCCTTGAAGAATACAGAAT
ATTTCAATCAACTAAAAAACAATAGCAACATAATTCTCCTGGGAGACTCCCAAGGGGACTTAAAAATGGCAGATGGAGTA
GCCAATGTGGAACACATCCTGAAAATTGGGTATCTAAATGATAGAGTGGATGAGCTTTTAGAAAAGTACATGGACTCTTA
TGATATTGTTCTAGTAAAAGATGAATCACTGGATGTAGCCAACTCTATCTTACAGAAGATTCTA

Alignment

ORF - retro_btau_1465 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.57 %
• Parental protein coverage: 96.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKMMPEIQKNSVHIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPSCHNVIDNCKLITD
          ..MMPEIQKNSVHIKNPTR.EEIICGLIKGGAAKLQIITDFDMTLS.FSYKGKRCPSCHNVIDN.KLITD
Retrocopy IEMMPEIQKNSVHIKNPTRIEEIICGLIKGGAAKLQIITDFDMTLSQFSYKGKRCPSCHNVIDNYKLITD

Parental  ECREKLLQLKEKYYAIEVDPLLTIEEKYPYIVEWYTKSHSLLVEQALPKAKLKEIVEESDIMLKEGYENF
          ECREKLLQLKEKYYAIEVDP.LTIEEKYPYIVEWYTKSHSLLVEQALPKAKLKEIVEESDIMLKEGYENF
Retrocopy ECREKLLQLKEKYYAIEVDPVLTIEEKYPYIVEWYTKSHSLLVEQALPKAKLKEIVEESDIMLKEGYENF

Parental  FDKLQQYGIPVFIFSAGIGDVLEEVIRQAGVYYPNVKVVSNFMDFDDNGLLKGFKGELIHVFNKHDGSLK
          FDKLQQY.IPVFIFSAGIGDVLEEVIRQAGVYYPNVKVVSNFMDFDDNGLLKGFKGELIHVFNKHDGSLK
Retrocopy FDKLQQYSIPVFIFSAGIGDVLEEVIRQAGVYYPNVKVVSNFMDFDDNGLLKGFKGELIHVFNKHDGSLK

Parental  NTEYFNQLKNNSNIILLGDSQGDLKMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKDESLDVA
          NTEYFNQLKNNSNIILLGDSQGDLKMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKDESLDVA
Retrocopy NTEYFNQLKNNSNIILLGDSQGDLKMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKDESLDVA

Parental  NSILQKIL
          NSILQKIL
Retrocopy NSILQKIL

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	0.07 RPM	26.60 RPM
ERP005899_muscle	0.16 RPM	47.72 RPM
SRP017611_brain	0.00 RPM	13.16 RPM
SRP017611_kidney	0.30 RPM	54.35 RPM
SRP017611_liver	0.00 RPM	3.78 RPM
SRP030211_testis	0.02 RPM	5.36 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1465 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1465 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465 ,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,