RetrogeneDB ID: retro_btau_1263

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:27508059..27508568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALSL
• Ensembl ID: ENSBTAG00000000156
• Aliases: None
• Description: lectin, galactoside-binding-like [Source:RefSeq peptide;Acc:NP_001192760]

Sequence

>retro_btau_1263
GGGTCTGTGGCCGACAGCGATGCAGTGGTGAACTAGATGATGCGCATTTAAACAACTCCTTGGGCTCTCCAGTTCAAGCC
GACATATACTTGCCATGACTGAGAGTGCTATTTTGTGGGCACATTAGAGGTGGCATGAGACCAGGCAAGAAAGTGTTAGT
GATGGGCATTGTAAACCTCAACCCAGAGAGCTTTGCCATCAGATTGACCTGTGGTGATTTGGAAGATCCTCCCGCAGAGG
TGGCAATTGAACTCAAAGCGGTGTTCACAGATCGGCAGCGACTCAGAAATTCTTGTATATTTGGGGAAAGAGGTGAAGAA
CAGTCAGCGATCCCTTACTTCCCATTCATCCCAGACCAGCCATTCAGGATGGAAATCCTTTGTTAGCATCCGGGTTTCAG
AGTGTTTGTGGATGGACAAACACTTTTTGATTTTTACCACCGCATTCAAACGTTATCTGCAATGGACACCATAAAGATCA
ATGGAGACCTCCAGATCACTAAGCTTGGC

Alignment

ORF - retro_btau_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSVADSDAVV-KLDDGHLNNSLGSPVQADVYFPRLIVPFCGHIKGGMRPGKKVLVMGIVDLNPESFAISL
          GSVADSDAVV..LDD.HLNNSLGSPVQAD.Y.P.L.V.FCGHI.GGMRPGKKVLVMGIV.LNPESFAI.L
Retrocopy GSVADSDAVV<ELDDAHLNNSLGSPVQADIYLP*LRVLFCGHIRGGMRPGKKVLVMGIVNLNPESFAIRL

Parental  TCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDG
          TCGD.EDPPA.VAIELKAVFTDRQ.LRNSCI.GERGEEQSAIPYFPFIPDQPFR.EILC.HP.FRVFVDG
Retrocopy TCGDLEDPPAEVAIELKAVFTDRQRLRNSCIFGERGEEQSAIPYFPFIPDQPFRMEILC*HPGFRVFVDG

Parental  HQLFDFYHRIQTLSAIDTIKINGDLQITKLG
          ..LFDFYHRIQTLSA.DTIKINGDLQITKLG
Retrocopy QTLFDFYHRIQTLSAMDTIKINGDLQITKLG

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	0.43 RPM
ERP005899_muscle	0.00 RPM	3.17 RPM
SRP017611_brain	0.00 RPM	10.10 RPM
SRP017611_kidney	0.00 RPM	12.45 RPM
SRP017611_liver	0.00 RPM	2.19 RPM
SRP030211_testis	0.00 RPM	55.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1263 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263 ,
Bos taurus	ENSBTAG00000016312	1 retrocopy	retro_btau_1069,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,