RetrogeneDB ID: retro_btau_247

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:21948511..21948937(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000026505
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSBTAG00000013761
• Aliases: None
• Description: Stathmin [Source:UniProtKB/Swiss-Prot;Acc:Q3T0C7]

Sequence

>retro_btau_247
ATGGCTTCTTCTGATATCCAGGTGAAGAAACTGGAGAAGCCTTCCTCAGGCCAGGCTTTTGAGCTGACTCTCAGCCCTCA
ATCAAAAGAATCTGTCCCAGAATTTCCCCTTTCCCCTCCCAAGAAGGATCTTTCCCTGGAGGAAATTCAGAAGAAATTAG
AAGCTGCAGAAGAAAGACGCAAGTCCCATGAAGCTGAGGTCTTGAAGCAGCTTGCTGAGAAAGGGGAGCCCGAGAAAGAA
GTGCTTCAGAAAGCGATAGAGGACAACTTCAGTAAAATGGCGGAAGAGAAGCTGACCCACAAGATGGAAGCCAATAAAGA
GAACAGAGAGGCACAGACGGCCACCAAGCTGAAGGACAAGCACGTTGAAGAAGTGAGGAAGAACAAAGAATCCAAAGACC
CTGCTGATGAGACTGAAGCCGACTAA

Alignment

ORF - retro_btau_247 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLK
          MASSDIQVK.LEK..SGQAFEL.LSP.SKESVPEFPLSPP.KKDLSLEEIQKKLEAAEERRKSHEAEVLK
Retrocopy MASSDIQVKKLEKPSSGQAFELTLSPQSKESVPEFPLSPP-KKDLSLEEIQKKLEAAEERRKSHEAEVLK

Parental  QLAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESK
          QLAEK.E.EKEVLQKAIE...NFSKMAEEKLTHKMEANKENREAQ.A.KL................K...
Retrocopy QLAEKGEPEKEVLQKAIED--NFSKMAEEKLTHKMEANKENREAQTATKLKDKHVEE--VRKNKESKDPA

Parental  DPADETEAD
          D...ETEAD
Retrocopy D---ETEAD

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	6.13 RPM
ERP005899_muscle	0.05 RPM	73.43 RPM
SRP017611_brain	0.00 RPM	225.84 RPM
SRP017611_kidney	0.00 RPM	14.17 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP030211_testis	0.36 RPM	223.52 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_247 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_247 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247 ,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,