RetrogeneDB ID: retro_ecab_240

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:47119603..47120471(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002748
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSECAG00000018072
• Aliases: None
• Description: leucine rich repeat containing 59 [Source:HGNC Symbol;Acc:28817]

Sequence

>retro_ecab_240
AAGCTGGACGGCAACGACCTGGACCTGAGCCTCAGCGACCCGAATGAGGTCCCCGTCAAGGAGCTTGCCGCCTTCCCAAA
GGCCACCCTACTGGATCTGTCCTGCAATAAAGTGATTACTCTACCGTCGGATTTCTGTGGCCTCAGGCACCTTGTGAAGC
TGGACCTCAGTAAGAACAAACTGCAGCAACTGTGGGCCGACTTCGGCCGTCTGGTCAACCTCCAGCACCTGGCTCTCCTC
AACAGGCTGCTCACCCTGTCTGTCAGATTTGCTCAGCTCAAGAGCCTGAAGTTGGCTGGACCTGAAGGATAACCCCCTGG
ATCCTGTCCTGGCCAAAGTGGCAGACGATTGCTTGGATGAGAAGCAGTGTAAGCAGTGTGCCAGCAAGGCGTGACAGCAC
ATGAAGGCCTTGCAGGCGAATCAGGGGCGAGAGAGGCTGCGGCGACTAGAAGTAGAACGAGAGAATGAGAGGAAGCGGGA
GGCCAGGCAGGGAGCTAAGGAAGCTCAGGAGCGGGAACTAGGGAAGCGGGAGAAGGCAGAAGAGAAGGAGCACCGGAGAA
AAGAGTATGATGCCTTCAAGGCAGCCAAGAGGGAGCGGGAGAAGAAACCTAAGAAGGAAACAAATCAGGCCACGAAATCT
AAGTCTGGCTCTCGCCCGCGGAAGCCACCACCCCGGAAACACACCCGGTCCTGGGCTGTGCTGAAGCTGCTGCTGCTGTG
CGTGGCCGGTGGGCTGGTTGCTTGTCGGGTGACAGAGCTGCAGCAGCAGCCCCTCTGCACCAGCGTGAACACCATCTACG
ACAGTGCGGTCCGGGGTCTGCGCAGCCAAGACATCCTCCAGTGGGTCCTGCAGACCGATTCTCAGCAG

Alignment

ORF - retro_ecab_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.41 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLDGNELDLSLSD-NEVP-KELAALPKATVLDLSCNKLTTLPSDFCGLTHLVKLDLSKNKLQQLPADFGR
          KLDGN.LDLSLSD.NEVP.KELAA.PKAT.LDLSCNK..TLPSDFCGL.HLVKLDLSKNKLQQL.ADFGR
Retrocopy KLDGNDLDLSLSDPNEVPVKELAAFPKATLLDLSCNKVITLPSDFCGLRHLVKLDLSKNKLQQLWADFGR

Parental  LVNLQHLDLLNNRLVTLPVSFAQLKSLK-WLDLKDNPLDPVLAKVAGDCLDEKQCKQCASKVLQHMKAVQ
          LVNLQHL.LLN.RL.TL.V.FAQLKSLK.WLDLKDNPLDPVLAKVA.DCLDEKQCKQCASK..QHMKA.Q
Retrocopy LVNLQHLALLN-RLLTLSVRFAQLKSLK>WLDLKDNPLDPVLAKVADDCLDEKQCKQCASKA*QHMKALQ

Parental  ADQERERQRRLEVEREAEKKREAKQRAKEAQEREVRKREKAEEKERRRKEYDALKAAKREQEKKPKKETN
          A.Q.RER.RRLEVERE.E.KREA.Q.AKEAQERE..KREKAEEKE.RRKEYDA.KAAKRE.EKKPKKETN
Retrocopy ANQGRERLRRLEVERENERKREARQGAKEAQERELGKREKAEEKEHRRKEYDAFKAAKREREKKPKKETN

Parental  QATKSKSGSRPRKPPPRKHTRSWAVLKLLLLLLLCVAGGLVACRVTELQQQPLCTSVNTIYDNAVRGLRS
          QATKSKSGSRPRKPPPRKHTRSWAVLKLLLL...CVAGGLVACRVTELQQQPLCTSVNTIYD.AVRGLRS
Retrocopy QATKSKSGSRPRKPPPRKHTRSWAVLKLLLL---CVAGGLVACRVTELQQQPLCTSVNTIYDSAVRGLRS

Parental  HNILQWVLQTDSQQ
          ..ILQWVLQTDSQQ
Retrocopy QDILQWVLQTDSQQ

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	1.00 RPM	32.94 RPM
SRP021940_cerebellum	0.88 RPM	30.59 RPM
SRP021940_embryo	2.53 RPM	60.94 RPM
SRP021940_placental_villous	1.06 RPM	34.93 RPM
SRP021940_synovial_membrane	1.98 RPM	52.79 RPM
SRP021940_testis	2.62 RPM	74.94 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_240 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_240 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240 ,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,