RetrogeneDB ID: retro_ecab_655

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:13346797..13347460(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015171
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSECAG00000020188
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_ecab_655
ATCTTTTTGAGAATGGAAACGACCCAGGTTCAGACTACGCTGGTGGCTCTAGCAGGTCTGGCTAAAACAAAAGGATTCCA
TACAACCATTGACGTTGGAGTTAAGTATGCAGAAAAACAAACAAGACGTTTTGATGAAGGAAAATTAAAGGCTGGCCAGA
GTGTAATTGGTTTGCAGATGGGAACCAACAAATGCGCCAGCCAAGCAGGTATGACAGCCTATGGGACTAGGAGGCATCTT
TATGATCCCAAAATGCAAACTGACAAACCTTTTGACCAGACCACGATTAGTCTGCAGATGGGCACCAACAAAGGAGCCAG
CCAGGCGGGGATGTTAGCGCCGGGTACCAGGAGAGACATCTACGATCAGAAGCTAACATTACAACCAGTGGACAACTCGA
CAATTTCTCTACAGATGGGTACCAACAAAGTCGCTTCCCAGAAAGGAATGAGTGTGTATGGGCTGGGGCCGCAAGTATAT
GATCCCAAATACTGTGCTGCTCCAACAGAACCTGTCATTCACAATGGAAGCCAAGGAACAGGAACAAATGGGTCGGAAAT
CAGTGATAGTGATTATCAGGCAGAATACCCAGAAGAATATCATGGCGAGTACCAAGATGCCTACCCCAGAGATTACCAAT
ATGGCGACCAAGGCCTTGATTAT

Alignment

ORF - retro_ecab_655 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.48 %
• Parental protein coverage: 67.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFENGNMTQVQTTLVALAGLAKTKGFHTTIDVGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAG
          .F.....TQVQTTLVALAGLAKTKGFHTTIDVGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAG
Retrocopy IFLRMETTQVQTTLVALAGLAKTKGFHTTIDVGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAG

Parental  MTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMG
          MTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMG
Retrocopy MTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMG

Parental  TNKVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYQDDYPR
          TNKVASQKGMSVYGLG.QVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYP.EYHGEYQD.YPR
Retrocopy TNKVASQKGMSVYGLGPQVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPEEYHGEYQDAYPR

Parental  DYQYGDQGIDY
          DYQYGDQG.DY
Retrocopy DYQYGDQGLDY

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
SRP021940_articular_cartilage	0.30 RPM	36.78 RPM
SRP021940_cerebellum	0.16 RPM	19.99 RPM
SRP021940_embryo	0.51 RPM	93.62 RPM
SRP021940_placental_villous	0.24 RPM	45.51 RPM
SRP021940_synovial_membrane	0.66 RPM	59.74 RPM
SRP021940_testis	0.00 RPM	5.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_655 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_655 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655 ,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,