RetrogeneDB ID: retro_btau_860

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:24907695..24908361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.77236
• Ensembl ID: ENSBTAG00000009336
• Aliases: None
• Description: latexin [Source:RefSeq peptide;Acc:NP_001073809]

Sequence

>retro_btau_860
ATGGAAATCCCTCCGACCCACTACCCGGCCACCAGGGCGGCCTCAGTGGTAGAGAGCTGCATCAACTACCAGCAGGGGAC
TCCCCACAAGGTGTTTCTGGTGCAGACAGTCGAACAAGCCAGCCTGGAGGATATTCCAGGAAGAGGACATAAGTACTGCC
TTAAATTTTCTGTGGAAGAAATTATCCAAAAAGAAGTTACAGTGAACTGCACAGCTGAAGTACTGTACCGTCCAACGGGA
CAAGATACTGCACCAGAAGTCAACTTAACATTTGAAGGAGAAATTGGAAAAAACCCAGATGAAGAAGATAACACATTTTA
TCAAAGACTCAAATCCATGTAGGAACCACTAGACGCACAAAATATTCCAGACAGTTTTGGAAATGTACCTCCAGAAATGA
AGCCAGTTCGACATTTAGCCTGGGTTGCCAGTGGTTATATAATATGGCAAAATTCTACTGAAAATACATGGTATAAAATG
GCAAAAATTCAAACTGTCAAGCAAGTGCAAAGAAATGATGACTTCATCGAGTTAGACTACACTATTCTCCTTCATGACAT
TGCATCTCAGGAGATTATTCCTTGGCAAATGCAAGTTCTCTGGCATCCACAATATGGTACTAAAGTAAAACATAATAGCC
ATCTGCCAAAGGAAGCACAATTGGAA

Alignment

ORF - retro_btau_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEIPPTHYPAARAASVVESCINYQQGTPHKLFLVQTVEQASLEDIPGRGHKYRLKFSVEEIIQKEVTVNC
          MEIPPTHYPA.RAASVVESCINYQQGTPHK.FLVQTVEQASLEDIPGRGHKY.LKFSVEEIIQKEVTVNC
Retrocopy MEIPPTHYPATRAASVVESCINYQQGTPHKVFLVQTVEQASLEDIPGRGHKYCLKFSVEEIIQKEVTVNC

Parental  TAEVLYPPTGQDTAPEVNFTFEGEIGKNPDEEDNTFYQRLKSMKEPLDAQNIPDSFGNVPPEMKPVRHLA
          TAEVLY.PTGQDTAPEVN.TFEGEIGKNPDEEDNTFYQRLKSM.EPLDAQNIPDSFGNVPPEMKPVRHLA
Retrocopy TAEVLYRPTGQDTAPEVNLTFEGEIGKNPDEEDNTFYQRLKSM*EPLDAQNIPDSFGNVPPEMKPVRHLA

Parental  WVASGYIIWQNSTENTWYKMAKIQTVKQVQRNDDFIELDYTILLHDIASQEIIPWQMQVLWHPQYGTKVK
          WVASGYIIWQNSTENTWYKMAKIQTVKQVQRNDDFIELDYTILLHDIASQEIIPWQMQVLWHPQYGTKVK
Retrocopy WVASGYIIWQNSTENTWYKMAKIQTVKQVQRNDDFIELDYTILLHDIASQEIIPWQMQVLWHPQYGTKVK

Parental  HNSRLPKEAQLE
          HNS.LPKEAQLE
Retrocopy HNSHLPKEAQLE

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	1.51 RPM
ERP005899_muscle	0.00 RPM	10.77 RPM
SRP017611_brain	0.00 RPM	7.35 RPM
SRP017611_kidney	0.06 RPM	8.59 RPM
SRP017611_liver	0.00 RPM	0.60 RPM
SRP030211_testis	0.02 RPM	4.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_860 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860 ,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,