RetrogeneDB ID: retro_btau_478

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:74118088..74118595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYF2
• Ensembl ID: ENSBTAG00000001651
• Aliases: None
• Description: None

Sequence

>retro_btau_478
GTGGGTGGAGCAGAGGAGCAGCAGCCTCCTGCAGGAGCCGAGGAGCTGGCCTCCCAGAAGCGAGAACAGAGGCTGCGCAA
ATTCCGGAAGCTGCACCGGAAGCGGAATGAAGCTCGTAAATTAAATCACCAGGAAGTTGTTGAAGAAAATAAAAGACTTA
AGTTACCTGCAAATTTGGAAGCCAAAAAGGCTCGTTTGGAATGGGAACTACAGGAAGAAGAAAAGAAAAAGGAATGTGCA
GCAAGAGGGGAAGACTATGAGAAAGTGAAGTTGCTAGAAATCAGTGCAGAAGATGCAGAAAGATGGGAGAGAAAAAAGAG
GAGGAAAAACCCCGACCTGGGATTTTCAGATTATGCTGCTGCCCAGCTTCGCCAGTATCATCGGCTGACCAAACAGATCA
AACCAGACATGGAAACATATGAGAAACTGAGAGAAAAGCATGGAGAAGAGTTTTTCCCAACGTCCAACAGTCTTCTTCAT
GGGACACATGTGCCTTCCACAGAGGAA

Alignment

ORF - retro_btau_478 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.04 %
• Parental protein coverage: 71.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGGAEEQQPPAGAEELASQKREQRLRKFRELHLKRNEARKLNHQEVVEEDKRLKLPANWEAKKARLEWEL
          VGGAEEQQPPAGAEELASQKREQRLRKFR.LH.KRNEARKLNHQEVVEE.KRLKLPAN.EAKKARLEWEL
Retrocopy VGGAEEQQPPAGAEELASQKREQRLRKFRKLHRKRNEARKLNHQEVVEENKRLKLPANLEAKKARLEWEL

Parental  QEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKRRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMETY
          QEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKRRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMETY
Retrocopy QEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKRRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMETY

Parental  ERLREKHGEEFFPTSNSLLHGTHVPSTEE
          E.LREKHGEEFFPTSNSLLHGTHVPSTEE
Retrocopy EKLREKHGEEFFPTSNSLLHGTHVPSTEE

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	26.03 RPM
ERP005899_muscle	0.48 RPM	16.26 RPM
SRP017611_brain	0.59 RPM	19.46 RPM
SRP017611_kidney	0.71 RPM	30.82 RPM
SRP017611_liver	0.23 RPM	16.23 RPM
SRP030211_testis	0.81 RPM	36.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_478 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478 ,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,