RetrogeneDB ID: retro_cfam_43

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:40844141..40845143(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015024
• Aliases: LOC403708, CCL, CTSL, CTSL1, CTSL2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CTSL1
• Ensembl ID: ENSCAFG00000001149
• Aliases: None
• Description: Cathepsin L1 Cathepsin L1 heavy chain Cathepsin L1 light chain [Source:UniProtKB/Swiss-Prot;Acc:Q9GL24]

Sequence

>retro_cfam_43
ATGAATCCTTCACTCTTCTTGACTGCCCTTTGCTTGGGAATAGCCTCAGCAGCTCCCAAATTTGATCAAAGCTTAAATGC
ACAGTGGTACCAGTGGAAGGCAACGCACAGGAGATTATATGGCATGAATGAAGAAGGATGGAGGAGAGCAGTGTGGGAGA
AGAATATGAAAATGATTGAACTGCATAATCGGGAATACAGCCAAGGGAAACATGGCTTCACAATGGCAATGAATGCCTTT
GGTGACATGACCAATGAAGAATTCAGGCAGGTGATGAATGGCTTTCAAAACCAGAAGCACAAGAAAGGGAAAATGTTCCA
AGAACCTCTCTTTGCTGAGATCCCCAAATCAGTGGACTGGAGAGAGAAAGGCTATGTAACTCCTGTGAAGAATCAGGGTC
AGTGTGGTTCTTGTTGGGCTTTTAGTGCAACTGGTGCCCTTGAAGGACAGATGTTCCGGAAAACGGGCAAACTTGTGTCA
CTGAGTGAGCAAAACCTGGTGGACTGCTCTAGGGCTCAAGGTAACGAGGGCTGCAATGGTGGCCTGATGGATAACGCCTT
CCGGTATGTTAAGGACAATGGAGGCCTGGACTCAGAGGAATCTTATCCGTATCTTGGAAGGGACACAGAGACCTGCAATT
ACAAGCCTGAGTGTTCTGCTGCCAATGACACTGGCTTTGTGGACCTCCCTCAACGGGAGAAGGCCCTAATGAAAGCAGTG
GCAACTCTAGGGCCCATCTCTGTTGCTATTGATGCAGGCCATCAGTCTTTCCAATTCTACAAATCAGGCATTTATTTTGA
TCCAGACTGCAGCAGCAAAGATCTAGATCATGGTGTTCTGGTGGTTGGCTATGGCTTTGAAGGAACAGATTCAAATAATA
AATTTTGGATTGTCAAGAACAGTTGGGGTCCAGAATGGGGCTGGAATGGCTATGTAAAAATGGCCAAAGACCAGAACAAC
CACTGTGGAATTGCCACAGCAGCCAGCTATCCCACTGTGTGA

Alignment

ORF - retro_cfam_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MNPSLFLTALCLGIASAAPKFDQSLNAQWYQWKATHRRLYGMNEEGWRRAVWEKNMKMIELHNREYSQGK
          MNPSLFLTALCLGIASAAPKFDQSLNAQWYQWKATHRRLYGMNEEGWRRAVWEKNMKMIELHNREYSQGK
Retrocopy MNPSLFLTALCLGIASAAPKFDQSLNAQWYQWKATHRRLYGMNEEGWRRAVWEKNMKMIELHNREYSQGK

Parental  HGFTMAMNAFGDMTNEEFRQVMNGFQNQKHKKGKMFQEPLFAEIPKSVDWREKGYVTPVKNQGQCGSCWA
          HGFTMAMNAFGDMTNEEFRQVMNGFQNQKHKKGKMFQEPLFAEIPKSVDWREKGYVTPVKNQGQCGSCWA
Retrocopy HGFTMAMNAFGDMTNEEFRQVMNGFQNQKHKKGKMFQEPLFAEIPKSVDWREKGYVTPVKNQGQCGSCWA

Parental  FSATGALEGQMFRKTGKLVSLSEQNLVDCSRAQGNEGCNGGLMDNAFRYVKDNGGLDSEESYPYLGRDTE
          FSATGALEGQMFRKTGKLVSLSEQNLVDCSRAQGNEGCNGGLMDNAFRYVKDNGGLDSEESYPYLGRDTE
Retrocopy FSATGALEGQMFRKTGKLVSLSEQNLVDCSRAQGNEGCNGGLMDNAFRYVKDNGGLDSEESYPYLGRDTE

Parental  TCNYKPECSAANDTGFVDLPQREKALMKAVATLGPISVAIDAGHQSFQFYKSGIYFDPDCSSKDLDHGVL
          TCNYKPECSAANDTGFVDLPQREKALMKAVATLGPISVAIDAGHQSFQFYKSGIYFDPDCSSKDLDHGVL
Retrocopy TCNYKPECSAANDTGFVDLPQREKALMKAVATLGPISVAIDAGHQSFQFYKSGIYFDPDCSSKDLDHGVL

Parental  VVGYGFEGTDSNNKFWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAASYPTV
          VVGYGFEGTDSNNKFWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAASYPTV
Retrocopy VVGYGFEGTDSNNKFWIVKNSWGPEWGWNGYVKMAKDQNNHCGIATAASYPTV

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
SRP012049_cerebellum	0.92 RPM	16.55 RPM
SRP017611_brain	0.56 RPM	16.99 RPM
SRP017611_kidney	4.29 RPM	77.07 RPM
SRP017611_liver	5.00 RPM	67.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_43 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_43 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001149	1 retrocopy	retro_cfam_43 ,
Echinops telfairi	ENSETEG00000007977	1 retrocopy	retro_etel_1465,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Vicugna pacos	ENSVPAG00000004397	1 retrocopy	retro_vpac_433,