RetrogeneDB ID: retro_fcat_1280

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:85344653..85345151(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALSL
• Ensembl ID: ENSFCAG00000001209
• Aliases: None
• Description: lectin, galactoside-binding-like [Source:HGNC Symbol;Acc:25012]

Sequence

>retro_fcat_1280
GACAGCGCTCCCACGGTGAAACTAAATGATGGGCATTTAAACAACTCCCTGGGCTCCCCAGTTCAAGCCATGTATTTCCC
AAGACTGATAGTTCCATTTTGTGGGCACATTACAGGTGGCATGAGACCAGGCAAGAAGCTGTTGGTGGTGGGGGCATCGT
AGACTTCAACCCAGAGAGCTTTGCTATCAGCTTGACCTGGGGTGACTCTGAAGACCCTTCTGCCAATGTGGCAATTGAAC
TCAAAGCTGGGTTCACAGACTGGCAACGACTCAGAAATTCTTGTATATCTAGGGAAAGAGGTGAAGGGCAGTCTGCGATA
CCTTACTTCCCATTCATCCCAGACCAGCTATTCAGGGTGGAAATTCTTTGTGAGCACCCATGTTTCAGAGCGTTTGTGGA
TGGACACCAATTTTTTTATTTTTATCACCACATTAAAATGTTATCTGCAGTTGGACACCATAAAGATACATGGGGACCTC
CAGATCGCTAAGCTTGGC

Alignment

ORF - retro_fcat_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.37 %
• Parental protein coverage: 95.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSDAAVKLDDGHLNNSLGSPVQADVYFPRLIVPFCGHIKGGMRPGKKVLVMGIV-DLNPESFAISLTCG-
          DS...VKL.DGHLNNSLGSPVQA..YFPRLIVPFCGHI.GGMRPGKK.LV.G....L.P......L..G.
Retrocopy DSAPTVKLNDGHLNNSLGSPVQA-MYFPRLIVPFCGHITGGMRPGKKLLVVGAS>RLQPRELCYQLDLG>

Parental  DSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQL
          DSEDP.A.VAIELKA.FTD.Q.LRNSCIS.ERGE.QSAIPYFPFIPDQ.FRVEILCEHP.FR.FVDGHQ.
Retrocopy DSEDPSANVAIELKAGFTDWQRLRNSCISRERGEGQSAIPYFPFIPDQLFRVEILCEHPCFRAFVDGHQX

Parental  FDFYHRIQTLSAI-DTIKINGDLQITKLG
          ....H.I..LSA..DTIKI.GDLQI.KLG
Retrocopy XXXXHHIKMLSAV>DTIKIHGDLQIAKLG

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
SRP017611_brain	0.00 RPM	8.61 RPM
SRP017611_kidney	0.00 RPM	3.81 RPM
SRP017611_liver	0.00 RPM	3.03 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1280 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1280 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280 ,
Felis catus	ENSFCAG00000024418	1 retrocopy	retro_fcat_838,
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,