RetrogeneDB ID: retro_cfam_1172

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:3735216..3736313(-)
• Located in intron of: ENSCAFG00000006124

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSCAFG00000014672
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_cfam_1172
ACTACTCTGAGCGTCCTGCTGGGTGTGGATCTGGGCAGTATGGATGAGGAAGAGGAAGTTGGAACACCTCCCCCACCTCC
TCCTCCCAGGAAGGACACCAAGCCAGAGCCAATGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCGCTGAAAGAGAAAG
AGCTAGGGAACGAAGCCTACAAGAAGAAAGACTTTGACACAGCCTTGAAGCACTATGACAGAACCAAGAACCTGGACCCC
ACCAAAATGACTTACATGACCAATCAAGTAGCTGTGTACTTCGAGAAGGGCAACTACTGTAAATGCGGGGAGCTTTGTGA
GAAGGCCATCGAAGTGGGGCGAGAAAACTGGGACTATCACAGATTGCCAAAGCTTATGCTCGAATTGGCAACTCCTACTT
CAAGGAAGAAAAGTACAAGTCTGCCATCCATTTCTATAACAAGTCTTTGGCAGAGCACCGGACCCCAGATGTGCTCAAGA
AATGCCAACAGGCAGAGAAAATTCTGAAGGAGCAAGAGCGGCTGGCTTACATAAACCCAGATCTGGCCTTGAAGGAGAAG
AACAAAGGCAATGAATGTTTTCAGAAAGGGGACTATCCCCAGGCCATGAAGCATTATACAGAAGCCATCAGACGGAATCC
AAAAGATGCCAAATTGTACAGCAATCGAGCTGCCTGCTACACCAAACTCCTGGAGTTTCAGCTGGCGCTCAAGGACTGTG
AGGAATGTATCCAGCTAGAGCCGGCCTTCATCAAGGGGTACACTCGGAAAGCAGCTGCCCTGGAGGCAATGAAGGACTAC
AGAAAAGCCATGGATGTCTACCAGAAGGCGTTAGATTTGGACTCCAACTGTAAGGAAGCAGCAGACAGTTACCAGCACTG
TATGATGGCCCAGTACAACCGCCACAAGAGCCCCAAAGACGTGAAGCGATGGGCCATGGCTGACCCTGAGGTGCAGCAGA
TAATGAGTGACCCGGCCATGTGGCTTATCCTGGAGCAGATGCAGAAGGACCCTCAGGCACTCAGCGAACACTTAAAAAAT
CCTGTAATAACACAGAAGATCCAGAAGCTGATGGATGTGGGTCTGACTGCAATTCGG

Alignment

ORF - retro_cfam_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.48 %
• Parental protein coverage: 67.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTLSVLLGVDLGSMDEEEEVGTPPPPPPPKKDTKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALK
          TTLSVLLGVDLGSMDEEEEVGTPPPPPPP.KDTKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALK
Retrocopy TTLSVLLGVDLGSMDEEEEVGTPPPPPPPRKDTKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALK

Parental  HYDRAKDLDPTNMTYMTNQAAVYFEKGDYSKCRELCEKAIEVGRENREDYR-QIAKAYARIGNSYFKEEK
          HYDR.K.LDPT.MTYMTNQ.AVYFEKG.Y.KC.ELCEKAIEVGREN..DY..QIAKAYARIGNSYFKEEK
Retrocopy HYDRTKNLDPTKMTYMTNQVAVYFEKGNYCKCGELCEKAIEVGRENW-DYH<QIAKAYARIGNSYFKEEK

Parental  YKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTE
          YK.AIHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLAL.EKNKGNECFQKGDYPQAMKHYTE
Retrocopy YKSAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALKEKNKGNECFQKGDYPQAMKHYTE

Parental  AIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPAFIKGYTRKAAALEAMKDYTKAMDVYQKAL
          AI.RNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPAFIKGYTRKAAALEAMKDY.KAMDVYQKAL
Retrocopy AIRRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPAFIKGYTRKAAALEAMKDYRKAMDVYQKAL

Parental  DLDSNCKEAADGYQRCMMAQYNRHDSPEDVKRRAMADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNP
          DLDSNCKEAAD.YQ.CMMAQYNRH.SP.DVKR.AMADPEVQQIMSDPAM.LILEQMQKDPQALSEHLKNP
Retrocopy DLDSNCKEAADSYQHCMMAQYNRHKSPKDVKRWAMADPEVQQIMSDPAMWLILEQMQKDPQALSEHLKNP

Parental  VIAQKIQKLMDVGLIAIR
          VI.QKIQKLMDVGL.AIR
Retrocopy VITQKIQKLMDVGLTAIR

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	0.21 RPM	101.39 RPM
SRP017611_brain	0.71 RPM	99.08 RPM
SRP017611_kidney	0.20 RPM	53.82 RPM
SRP017611_liver	0.22 RPM	29.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1172 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1172 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172 , retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,