RetrogeneDB ID: retro_cfam_1477

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:25066571..25067554(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPT2
• Ensembl ID: ENSCAFG00000012960
• Aliases: None
• Description: septin 2 [Source:HGNC Symbol;Acc:7729]

Sequence

>retro_cfam_1477
CACCAAAAATCAGTGAAAAAAGGTTTTGAGTTCACACTAATGTTGGTCGGTGAATGGGGTCTAGGAAAATCAACTCTCAT
AAACAGCCTATTCCTGACTGATCTCCACCCAGAAAGAATCATACCTGGAGCCGCAGAGAAAATTGAAAGAACTGTCCAGA
TTGAGGCTTCGACTGTGGACATGGAGGAGCGAGGGGTCAAGCTGCGCTTGACAGTGGTGGACACGCCTGGCGACGGGGAT
GCCATCAACTGCAGGGACTGTTTCAAGACCATCATCTCCTACACTGACGAGCAGTTTGAACGGTACCTGCAGGACGAGAG
TGGTTTGAACCGGCGGCACATCATCGATAACAGGGTGCACTGCTGCTTTTACTTCATCTCCCCCTTTGGACATGGACTTA
AGCCCTCAGACGTCGCATTCATGAAAGCAATACACAATAAGGAGAACATCGTGCCCGTCATTGCCAAAGCTGACACCCTC
ACCCTGAAGGAGCAGGAGCGCTTGAAGAAAAGAATTCTGATGAAACTGAAGAACGTAACATCAAAATCTACCACTTACCT
GATGCAGAATCAGATGAAGGTGAGGACTTTAAAGAGCAGACCAGACTTCTCAAGGCCAGTATCCCGTTCTCTGTGGTTGG
ATCCAATCAGCTGATTGAAGCCAAGGGCAAGAAGGTCAGAGGCCGCCTGTACCCGTGGGGTGTTGTGGAGGTGGAGAGCC
CGGAGCACAACGACTTCCTGAAGCTGCGGACAACGCTCATCACCCACATGCAGGATCTCCAGGAGGTGACCCAGGACCTT
CACTACGAAAACTTCCCTTCTGAGAGGCTCAAAAGAGGCGGCAGAAAAGTAGAAAATGAGGCCATGAATAAAGACCAGAT
CCTGCTGGAGAAGGAAGCAGAGCTCCGCCGCATGCAGGAGATGATCGCAAGGATGCAGGCTCAGATGCAGCTGCGGATGC
AGGGTGGGGATGCTGACGGTGGG

Alignment

ORF - retro_cfam_1477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.03 %
• Parental protein coverage: 93.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HRKSVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERIIPGAAEKIERTVQIEASTVEIEERGVKLRL
          H.KSVKKGFEFTLM.VGE.GLGKSTLINSLFLTDL.PERIIPGAAEKIERTVQIEASTV..EERGVKLRL
Retrocopy HQKSVKKGFEFTLMLVGEWGLGKSTLINSLFLTDLHPERIIPGAAEKIERTVQIEASTVDMEERGVKLRL

Parental  TVVDTPGYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVAF
          TVVDTPG.GDAINCRDCFKTIISY.DEQFERYL.DESGLNRRHIIDNRVHCCFYFISPFGHGLKP.DVAF
Retrocopy TVVDTPGDGDAINCRDCFKTIISYTDEQFERYLQDESGLNRRHIIDNRVHCCFYFISPFGHGLKPSDVAF

Parental  MKAIHNKVNIVPVIAKADTLTLKERERLKKRIL-DEIEEHNIKIYHLPDAESDEDEDFKEQTRLLKASIP
          MKAIHNK.NIVPVIAKADTLTLKE.ERLKKRIL.DE.EE.NIKIYHLPDAESDE.EDFKEQTRLLKASIP
Retrocopy MKAIHNKENIVPVIAKADTLTLKEQERLKKRIL<DETEERNIKIYHLPDAESDEGEDFKEQTRLLKASIP

Parental  FSVVGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLITHMQDLQEVTQDLHYENFRSERLKR
          FSVVGSNQLIEAKGKKVRGRLYPWGVVEVE.PEHNDFLKLRT.LITHMQDLQEVTQDLHYENF.SERLKR
Retrocopy FSVVGSNQLIEAKGKKVRGRLYPWGVVEVESPEHNDFLKLRTTLITHMQDLQEVTQDLHYENFPSERLKR

Parental  GASRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQLQMQGGDADGG
          G..RKVENE.MNKDQILLEKEAELRRMQEMIARMQAQMQL.MQGGDADGG
Retrocopy G-GRKVENEAMNKDQILLEKEAELRRMQEMIARMQAQMQLRMQGGDADGG

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	0.59 RPM	137.76 RPM
SRP017611_brain	0.79 RPM	96.62 RPM
SRP017611_kidney	0.59 RPM	82.81 RPM
SRP017611_liver	0.22 RPM	30.60 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1477 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477 ,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35,