RetrogeneDB ID: retro_acar_27

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:127025686..127026817(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000013643
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000017497
• Aliases: None
• Description: None

Sequence

>retro_acar_27
ATGAAGGACGTCCCTGGCTACCTGCAGCAGTCTCAGAGCTCGGGGCCAGGCCAGGCCGCCGTGTGCCACCGCCTGGAGGA
GCTCTACAACAAAAAACTCTGGCACCAACTGACTCTCCAGGTTTTGGACTTTGTTCAGGACCCCTGCTTTGCCCAAGGAG
ATGGGCTTATCAAGTTATATGAGAACTTCATCAGTGAATTTGAACACAGGGTGAACCCTTTGTCCCTTGTAGAAATTATT
CTTCATGTAGTACGACAGATGACAGATCCTAATGTGGCCCTTACTTTTCTGGAAAAGACCCGAGAAAAGGTGAAAAGCAG
TGATGAAGCTGTGATTCTTTGTAAAACAGCAATTGGGGCTCTGAAATTAAATATTGGTGACCTGCAAGTCACAAAGGAAA
CCATAGAAGAAGTTGAGGAGATGCTGAATAATCTGCCTGGTGTGACATCTATTCATAGCCGCTTTTATGACCTCTCCAGC
AAGTATTATCAGACAATCGGGAATCATGCCTCTTACTATAAGGATGCTCTAAGGTTTCTGGGATGTATAGATGTCAGAGA
TCTACCAGTGGCAGACCAGCAGGAGAGAGCCTTTACATTGGGCCTGGCAGGACTCCTTGGGGAAGGAGTCTATAACTTTG
GCGAACTGCTTATGCATCCAGTGCTGGAGTCTTTGAGGGACACTGACAGACAGTGGCTGATTGACACTCTTTATGCCTTC
AACAGTGGCAATGTGGAAAAATTCCAGGCTTTGAAGTCAGCATGGGGCCAGCAGCCAGACCTGGCTGCAAATGAAGCTCT
TCTGCTGCAAAAGATCCAGTTGCTTTGCCTCATGGAGATGACCTTCACCCGACCAGCTAACCACTGGCAACTCACTTTTG
AAGAGATTGCTAAAAGTGCCAAAGTCACTGTAAATGAGGTAGAGCTGCTAGTGATGAAAGCGCTTTCAGTAGGTTTGGTA
AAAGGCAGTATTGACGAAGTGGACAAAAAGGTTCACATGACTTGGGTCCAACCACGGGTGCTGGATTTACAACAGATAAA
GGGCATGAAAGTCCGCCTGGAGTTCTGGTGCACAGATGTTAAGAGCATGGAGATGTTGGTGGAGCACCAAGCCCATGATA
TCCTAACATAA

Alignment

ORF - retro_acar_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDVPGYLQQSQSSGPGQAAVWHRLEELYNKKLWHQLTLQVLDFVQDPCFAQGDGLIKLYENFISEFEHR
          MKDVPGYLQQSQSSGPGQAAV.HRLEELYNKKLWHQLTLQVLDFVQDPCFAQGDGLIKLYENFISEFEHR
Retrocopy MKDVPGYLQQSQSSGPGQAAVCHRLEELYNKKLWHQLTLQVLDFVQDPCFAQGDGLIKLYENFISEFEHR

Parental  VNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGALKLNIGDLQVTKETIEEVEE
          VNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGALKLNIGDLQVTKETIEEVEE
Retrocopy VNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGALKLNIGDLQVTKETIEEVEE

Parental  MLNNLPGVTSVHSRFYDLSSKYYQTIGNHASYYKDALRFLGCIDVRDLPVADQQERAFTLGLAGLLGEGV
          MLNNLPGVTS.HSRFYDLSSKYYQTIGNHASYYKDALRFLGCIDVRDLPVADQQERAFTLGLAGLLGEGV
Retrocopy MLNNLPGVTSIHSRFYDLSSKYYQTIGNHASYYKDALRFLGCIDVRDLPVADQQERAFTLGLAGLLGEGV

Parental  YNFGELLMHPVLESLRDTDRQWLIDTLYAFNSGNVEKFQALKSAWGQQPDLAANEALLLQKIQLLCLMEM
          YNFGELLMHPVLESLRDTDRQWLIDTLYAFNSGNVEKFQALKSAWGQQPDLAANEALLLQKIQLLCLMEM
Retrocopy YNFGELLMHPVLESLRDTDRQWLIDTLYAFNSGNVEKFQALKSAWGQQPDLAANEALLLQKIQLLCLMEM

Parental  TFTRPANHRQLTFEEIAKSAKVTVNEVELLVMKALSVGLVKGSIDEVDKKVHMTWVQPRVLDLQQIKGMK
          TFTRPANH.QLTFEEIAKSAKVTVNEVELLVMKALSVGLVKGSIDEVDKKVHMTWVQPRVLDLQQIKGMK
Retrocopy TFTRPANHWQLTFEEIAKSAKVTVNEVELLVMKALSVGLVKGSIDEVDKKVHMTWVQPRVLDLQQIKGMK

Parental  DRLEFWCTDVKSMEMLVEHQAHDILT
          .RLEFWCTDVKSMEMLVEHQAHDILT
Retrocopy VRLEFWCTDVKSMEMLVEHQAHDILT

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
SRP009831_adrenal	0.13 RPM	26.16 RPM
SRP009831_brain	0.14 RPM	37.49 RPM
SRP009831_dewlap	0.30 RPM	64.76 RPM
SRP009831_embryo	0.77 RPM	98.67 RPM
SRP009831_heart	0.00 RPM	40.88 RPM
SRP009831_liver	0.00 RPM	27.32 RPM
SRP009831_lung	0.00 RPM	28.06 RPM
SRP009831_ovary	0.12 RPM	73.93 RPM
SRP009831_skeletal_muscle	0.04 RPM	33.14 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_27 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_27 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017497	1 retrocopy	retro_acar_27 ,