RetrogeneDB ID: retro_cfam_13

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:17594079..17595597(-)
• Located in intron of: ENSCAFG00000010768

Retrocopy information

• Ensembl ID: ENSCAFG00000010789
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000001785
• Aliases: None
• Description: tRNA-splicing ligase RtcB homolog [Source:UniProtKB/TrEMBL;Acc:E2RCD6]

Sequence

>retro_cfam_13
ATGAGTCGCAGCTATAATGATGAGCTACAGTTCTTGGAAAAGATCAATAAAAACTGCTGGAGAATCAAGAAGGGCTTCGT
GCCCAACATGCAGGTGGAAGGTGTTTTCTATGTGAATGACGCTCTGGGAAAATTAATGTTTGAGGAATTAAGAAATGCCG
GTCGAGGTGGTGGTGTTGGTGGCTTCCTACCAGCCATGAAACAAACTGGCAACATGGCAGCCCTGCCTGGGATTGTTCAT
AGATCTATTGGGCTTCCTGATGTCCATTCAGGTTATGGGTTTGCTATTGGGAATATGGCAGCCTTTGATATGAATGACCC
CGAAGCAGTGGTATCCCCAGGTGGTGTCGGATTTGACATCAACTGTGGTGTCCGCTTGCTAAGAACCAATTTAGATGAAA
GTGGTGTCCAGCCTGTGAAGGAGCAGCTTGCCCAAACTATGTTTGACCACATTCCTGTTGGAGTGGGATCAAAAGGTGTC
ATCCCCATGAGTGCCAAAGACTTGGAGGAGGCCTTAGAGATGGGTGTGAATTGGTCCCTGAGGGAAGGCTATACCTGGGC
TGAGGACAAGGAGCACTGTGAGGAGTACGGCAGGATGTTGCAGGCTGACCCCAATAAAGTCTCTGCAAGGGCTAAGAAAA
GAGGCCTTCCTCAGTTGGGGACCCTGGGAGCAGGCAACCACTATGCAGAAATCCAGGTTGTGGATGAGATTTTCAATGAG
TATGCTGCTAAGAAAATGGGCATCGACCATAAGGGACAAGTGTGTGTGATGATCCACAGTGGAAGCAGAGGCTTGGGCCA
CCAAGTAGCCACAGATGCACTGGTAGCTATGGAAAAAGCCATGAAAAGAGACAAGATTATAGTCAACAACCGGCAGTTGG
CTTGTGCTCGGATTGCTTCCCCAGGGGGTCAGGACTACCTGAAGGGGATGGCAGCTGCTGGGAACTATGCCTGGGTCAAC
CGCTCTTCCATGACCTTCTTAACCCGTCAGGCTTTAGCCAAGGTCTTCAACACAACCCCTGATGACTTGGACCTACATGT
GATCTATGATGTTTCTCACAATATTGCCAAAGTAGAACAGCACGTGGTGGATGGAAAGGAACGGACACTGTTGGTACACA
GGAAGGGATCCACTCGGGCTTTCCCTCCTCACCATCCTCTCATTGCTGTGGATTACCAACTCACTGGACAGCTGATGCTC
ACTGGTGGCACCACGGGCACCTGCAGTTACGTTCTTACGGGCACCAAGCAGGGCATGACGGAGACCTTTGGGACCACTTG
CCATGGAGCGGGCTGTGCATTGTCCCGAGCAAAATCTCATCATAATTTAGATTTCCAGGATGTCTTGGACAAACTGGCAG
ATATGGGAATCGCAGTCCGAGTTGCCTCACCCAAACTGGTTATGGAAGAGGCTCCTGAGTCCTATAAGAATGTGACGGAT
GTGATGAACACCTGTCATGATGCTGGAATCAGCAAGAAGGCCATTAAACTGAGACCAACTGCTGTGATCAAAGGATAG

Alignment

ORF - retro_cfam_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRNACRGGGVGGFLPAMKQIG
          MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDAL.KLMFEELRNA.RGGGVGGFLPAMKQ.G
Retrocopy MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALGKLMFEELRNAGRGGGVGGFLPAMKQTG

Parental  NVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVK
          N.AALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDES.VQPVK
Retrocopy NMAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESGVQPVK

Parental  EQLAQAMFDHIPVGVGSKGVIPMSAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQADPNKVSAR
          EQLAQ.MFDHIPVGVGSKGVIPMSAKDLEEALEMGV.WSLREGY.WAEDKEHCEEYGRMLQADPNKVSAR
Retrocopy EQLAQTMFDHIPVGVGSKGVIPMSAKDLEEALEMGVNWSLREGYTWAEDKEHCEEYGRMLQADPNKVSAR

Parental  AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKA
          AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKA
Retrocopy AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKA

Parental  MKRDKIIVNDRQLACARIASPEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYD
          MKRDKIIVN.RQLACARIASP.GQDYLKGMAAAGNYAWVNRSSMTFLTRQA.AKVFNTTPDDLDLHVIYD
Retrocopy MKRDKIIVNNRQLACARIASPGGQDYLKGMAAAGNYAWVNRSSMTFLTRQALAKVFNTTPDDLDLHVIYD

Parental  VSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIGGTMGTCSYVLTGTEQGMT
          VSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQ..L.GGT.GTCSYVLTGT.QGMT
Retrocopy VSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQLMLTGGTTGTCSYVLTGTKQGMT

Parental  ETFGTTCHGAGRALSRAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGI
          ETFGTTCHGAG.ALSRAKS..NLDFQDVLDKLADMGIA.RVASPKLVMEEAPESYKNVTDV.NTCHDAGI
Retrocopy ETFGTTCHGAGCALSRAKSHHNLDFQDVLDKLADMGIAVRVASPKLVMEEAPESYKNVTDVMNTCHDAGI

Parental  SKKAIKLRPIAVIKG
          SKKAIKLRP.AVIKG
Retrocopy SKKAIKLRPTAVIKG

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	0.50 RPM	52.62 RPM
SRP017611_brain	0.64 RPM	43.11 RPM
SRP017611_kidney	0.66 RPM	71.19 RPM
SRP017611_liver	0.07 RPM	24.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_13 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_13 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011070	1 retrocopy	retro_btau_1682,
Canis familiaris	ENSCAFG00000001785	2 retrocopies	retro_cfam_13 , retro_cfam_977,
Myotis lucifugus	ENSMLUG00000007803	1 retrocopy	retro_mluc_1461,
Oryctolagus cuniculus	ENSOCUG00000008270	1 retrocopy	retro_ocun_1520,