RetrogeneDB ID: retro_btau_1554

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:2480058..2481011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.52594
• Ensembl ID: ENSBTAG00000008804
• Aliases: None
• Description: protein SAAL1 [Source:RefSeq peptide;Acc:NP_001192490]

Sequence

>retro_btau_1554
AACAAGCAGATTGTTACTTGCCTTTCCCAGACAGGAGTGGCCAGTGTCTGGGTTGAAAGAATCCGAGAAAATCCAGCTAT
TTATGATAGCATTTGCTTCATCATGTCAAGTTCAACAAATGTTGACTTGCTGGTAAAGGTTGGGGAGGTTGTGGACAAGC
TGTTTGATTTGGTTGAGAAGCTAATGTGGGAATAGATTAGAAGTGGGGCTGTTCAGGCTCTGGACCAACCCCAGGAAGAT
TCTGAACAGCAGCCAGTGTTTCGAATTGTGCCCTGTGTACTTGAAGCTGCCAAACAAGTGTACTCTGAAAATCCAGAAGG
GCTCGATGTTTACATGCATGTCTTACAGCTGCTCACCACAGTAGATGATGGAATTTAAGCAATTGTACAGTGTCCTGACA
CTGGGAAAGACACTTGGAATATAGTTTTTGATCTGGTGTGCCATGAATTCTGCCAGTCTGATGATCCGCCCATCATACTG
CAAGAAGAGAAAACAGTGCTGGCCTCTGATTTTTCAGTGTTGTCCGCCATCTATGCTTCACAGACTGAACAGGAGTATCT
AAAGATAGGAAAAGTGGATCTTCCTCTAGTTGACAGCCTGATTTGTGTCTTACAAAATATGGAACATTGTCAGAAGAACC
CAGAGAACTCAACGGAGTCTAACACAGAAGAAACTAAAAGTCTGATTTAACCCAAGATGGTTTCCACTTGAAAATCTTGA
ACAATATTTCATGTGAATTTCTTTCTAATATTTTCCAAGTATTAACAAAGGAGAAAGGTAACTCAGAGATTAGGGACAGC
AAGTTAAGCAAACAGAAGTGTTCCTGTGCATTTGAGACTCTTCTCCCTTTCTGTAGCCCTGTGGTGGAAGACTTTCTTAA
AATCCTCCGTGAAGTTGATAAGACCCTTGCTGGTAATCTGGAGGAAAAGTTCCCAAGTTTGAAGTTTCAGACT

Alignment

ORF - retro_btau_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRLLLTCLSQTEVASVWVERIRENPAIYDSICFIMSSSTNVDLLVKVGEVVDKLFDLDEKLMLEWIKSGA
          .....TCLSQT.VASVWVERIRENPAIYDSICFIMSSSTNVDLLVKVGEVVDKLFDL.EKLM.E.I.SGA
Retrocopy NKQIVTCLSQTGVASVWVERIRENPAIYDSICFIMSSSTNVDLLVKVGEVVDKLFDLVEKLMWE*IRSGA

Parental  VQALDQPQEDSEQQPVFRIVPCVLEAAKQVRSENPEGLDVYMHILQLLTTVDDGIQAIVQCPDTGKDTWN
          VQALDQPQEDSEQQPVFRIVPCVLEAAKQV.SENPEGLDVYMH.LQLLTTVDDGI.AIVQCPDTGKDTWN
Retrocopy VQALDQPQEDSEQQPVFRIVPCVLEAAKQVYSENPEGLDVYMHVLQLLTTVDDGI*AIVQCPDTGKDTWN

Parental  LLFDLVCHEFCQSDDPPIILQEQKTVLASVFSVLSAIYASQTEQEYLKIGKVDLPLIDSLIRVLQNMEHC
          ..FDLVCHEFCQSDDPPIILQE.KTVLAS.FSVLSAIYASQTEQEYLKIGKVDLPL.DSLI.VLQNMEHC
Retrocopy IVFDLVCHEFCQSDDPPIILQEEKTVLASDFSVLSAIYASQTEQEYLKIGKVDLPLVDSLICVLQNMEHC

Parental  QKKPENSVESNTEETK-KSDLTQEDFHLKILKDISCEFLSNIFQVLTKETITQGLKEGQLSKQKCSCAFE
          QK.PENS.ESNTEETK.KSDLTQ..FHLKIL..ISCEFLSNIFQVLTKE..........LSKQKCSCAFE
Retrocopy QKNPENSTESNTEETK<KSDLTQDGFHLKILNNISCEFLSNIFQVLTKEKGNSEIRDSKLSKQKCSCAFE

Parental  NLLPFYSPVVEDFLKILREVDKTLAGNLEEGFPSLKIQT
          .LLPF.SPVVEDFLKILREVDKTLAGNLEE.FPSLK.QT
Retrocopy TLLPFCSPVVEDFLKILREVDKTLAGNLEEKFPSLKFQT

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	3.24 RPM
ERP005899_muscle	0.05 RPM	5.75 RPM
SRP017611_brain	0.00 RPM	4.48 RPM
SRP017611_kidney	0.12 RPM	6.40 RPM
SRP017611_liver	0.00 RPM	3.25 RPM
SRP030211_testis	0.18 RPM	8.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1554 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008804	1 retrocopy	retro_btau_1554 ,